Starting phenix.real_space_refine on Thu Feb 15 05:39:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5s_16442/02_2024/8c5s_16442_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5s_16442/02_2024/8c5s_16442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5s_16442/02_2024/8c5s_16442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5s_16442/02_2024/8c5s_16442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5s_16442/02_2024/8c5s_16442_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c5s_16442/02_2024/8c5s_16442_updated.pdb" } resolution = 3.75 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= 0.018 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: 5 Type Number sf(0) Gaussians P 65 5.49 5 S 36 5.16 5 C 7038 2.51 5 N 1960 2.21 5 O 2213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 114": "OE1" <-> "OE2" Residue "B GLU 115": "OE1" <-> "OE2" Residue "B GLU 222": "OE1" <-> "OE2" Residue "B GLU 233": "OE1" <-> "OE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A PHE 826": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 926": "OE1" <-> "OE2" Residue "A GLU 999": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11312 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2758 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 316} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 7244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7244 Classifications: {'peptide': 924} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 44, 'TRANS': 879} Chain breaks: 2 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 80 Chain: "N" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 580 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "T" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 569 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 5} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.68, per 1000 atoms: 0.59 Number of scatterers: 11312 At special positions: 0 Unit cell: (104.76, 116.4, 119.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 65 15.00 O 2213 8.00 N 1960 7.00 C 7038 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.00 Conformation dependent library (CDL) restraints added in 2.0 seconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 9 sheets defined 50.2% alpha, 6.3% beta 23 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 6.13 Creating SS restraints... Processing helix chain 'B' and resid 8 through 13 Processing helix chain 'B' and resid 26 through 36 Processing helix chain 'B' and resid 38 through 41 No H-bonds generated for 'chain 'B' and resid 38 through 41' Processing helix chain 'B' and resid 45 through 47 No H-bonds generated for 'chain 'B' and resid 45 through 47' Processing helix chain 'B' and resid 59 through 68 Processing helix chain 'B' and resid 80 through 89 Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 144 through 156 removed outlier: 3.597A pdb=" N GLY B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 191 through 199 Processing helix chain 'B' and resid 211 through 214 Processing helix chain 'B' and resid 218 through 224 removed outlier: 4.070A pdb=" N GLU B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 233 No H-bonds generated for 'chain 'B' and resid 231 through 233' Processing helix chain 'B' and resid 256 through 265 Processing helix chain 'B' and resid 274 through 280 removed outlier: 4.204A pdb=" N MET B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ASP B 279 " --> pdb=" O ASN B 275 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N SER B 280 " --> pdb=" O THR B 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 274 through 280' Processing helix chain 'B' and resid 285 through 292 Processing helix chain 'B' and resid 296 through 299 No H-bonds generated for 'chain 'B' and resid 296 through 299' Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'A' and resid 388 through 394 Processing helix chain 'A' and resid 398 through 420 removed outlier: 5.057A pdb=" N ASP A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 441 removed outlier: 4.138A pdb=" N ALA A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 475 Proline residue: A 463 - end of helix removed outlier: 3.715A pdb=" N LEU A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 491 No H-bonds generated for 'chain 'A' and resid 488 through 491' Processing helix chain 'A' and resid 493 through 500 Proline residue: A 498 - end of helix Processing helix chain 'A' and resid 505 through 516 Processing helix chain 'A' and resid 531 through 551 Processing helix chain 'A' and resid 594 through 611 Processing helix chain 'A' and resid 653 through 661 Processing helix chain 'A' and resid 704 through 716 Processing helix chain 'A' and resid 720 through 731 Processing helix chain 'A' and resid 739 through 750 removed outlier: 3.847A pdb=" N LYS A 750 " --> pdb=" O GLN A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 812 Processing helix chain 'A' and resid 843 through 847 Processing helix chain 'A' and resid 861 through 873 removed outlier: 3.614A pdb=" N PHE A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 899 removed outlier: 3.796A pdb=" N HIS A 890 " --> pdb=" O PHE A 886 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN A 892 " --> pdb=" O GLU A 888 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASP A 893 " --> pdb=" O SER A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 908 through 910 No H-bonds generated for 'chain 'A' and resid 908 through 910' Processing helix chain 'A' and resid 914 through 929 Processing helix chain 'A' and resid 949 through 958 Processing helix chain 'A' and resid 962 through 967 Processing helix chain 'A' and resid 978 through 993 Processing helix chain 'A' and resid 999 through 1003 Processing helix chain 'A' and resid 1010 through 1022 removed outlier: 4.215A pdb=" N VAL A1021 " --> pdb=" O VAL A1017 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N TYR A1022 " --> pdb=" O MET A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1040 Proline residue: A1039 - end of helix Processing helix chain 'A' and resid 1048 through 1064 removed outlier: 4.974A pdb=" N GLU A1064 " --> pdb=" O SER A1060 " (cutoff:3.500A) Processing helix chain 'A' and resid 1068 through 1085 removed outlier: 3.536A pdb=" N ILE A1072 " --> pdb=" O SER A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1179 removed outlier: 4.246A pdb=" N LYS A1154 " --> pdb=" O ALA A1150 " (cutoff:3.500A) Proline residue: A1158 - end of helix removed outlier: 3.833A pdb=" N ALA A1167 " --> pdb=" O HIS A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1214 Processing helix chain 'A' and resid 1217 through 1228 Processing helix chain 'A' and resid 1243 through 1256 Processing helix chain 'A' and resid 1265 through 1280 Processing helix chain 'A' and resid 1284 through 1291 Processing helix chain 'A' and resid 1296 through 1299 No H-bonds generated for 'chain 'A' and resid 1296 through 1299' Processing helix chain 'A' and resid 1306 through 1310 removed outlier: 3.834A pdb=" N GLU A1310 " --> pdb=" O LEU A1306 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1306 through 1310' Processing helix chain 'A' and resid 1340 through 1344 Processing helix chain 'A' and resid 1347 through 1349 No H-bonds generated for 'chain 'A' and resid 1347 through 1349' Processing sheet with id= A, first strand: chain 'B' and resid 242 through 248 removed outlier: 4.516A pdb=" N LYS B 167 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LYS B 49 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N VAL B 135 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 51 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLN B 72 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ASP B 52 " --> pdb=" O GLN B 72 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N SER B 74 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N GLN B 96 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N GLU B 77 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU B 98 " --> pdb=" O GLU B 77 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 528 through 530 Processing sheet with id= C, first strand: chain 'A' and resid 614 through 616 Processing sheet with id= D, first strand: chain 'A' and resid 734 through 736 Processing sheet with id= E, first strand: chain 'A' and resid 822 through 824 Processing sheet with id= F, first strand: chain 'A' and resid 942 through 944 removed outlier: 3.648A pdb=" N THR A1193 " --> pdb=" O VAL A 942 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id= H, first strand: chain 'A' and resid 1127 through 1131 Processing sheet with id= I, first strand: chain 'A' and resid 1233 through 1236 424 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 5.74 Time building geometry restraints manager: 5.35 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: 3140 1.34 - 1.45: 2231 1.45 - 1.57: 6142 1.57 - 1.69: 133 1.69 - 1.81: 62 Bond restraints: 11708 Sorted by residual: bond pdb=" O3' DC T 24 " pdb=" P DG T 25 " ideal model delta sigma weight residual 1.607 1.728 -0.121 1.50e-02 4.44e+03 6.56e+01 bond pdb=" O3' DT N 135 " pdb=" P DG N 136 " ideal model delta sigma weight residual 1.607 1.495 0.112 1.50e-02 4.44e+03 5.56e+01 bond pdb=" O3' DC T 17 " pdb=" P DA T 18 " ideal model delta sigma weight residual 1.607 1.499 0.108 1.50e-02 4.44e+03 5.16e+01 bond pdb=" O3' DA T 31 " pdb=" P DT T 32 " ideal model delta sigma weight residual 1.607 1.506 0.101 1.50e-02 4.44e+03 4.56e+01 bond pdb=" O3' DA T 34 " pdb=" P DA T 35 " ideal model delta sigma weight residual 1.607 1.523 0.084 1.50e-02 4.44e+03 3.15e+01 ... (remaining 11703 not shown) Histogram of bond angle deviations from ideal: 90.69 - 99.70: 32 99.70 - 108.71: 1195 108.71 - 117.72: 7898 117.72 - 126.73: 6639 126.73 - 135.74: 376 Bond angle restraints: 16140 Sorted by residual: angle pdb=" C3' DA T 35 " pdb=" O3' DA T 35 " pdb=" P DT T 36 " ideal model delta sigma weight residual 120.20 99.37 20.83 1.50e+00 4.44e-01 1.93e+02 angle pdb=" C3' A C 104 " pdb=" O3' A C 104 " pdb=" P A C 105 " ideal model delta sigma weight residual 120.20 101.23 18.97 1.50e+00 4.44e-01 1.60e+02 angle pdb=" C3' DC T 17 " pdb=" O3' DC T 17 " pdb=" P DA T 18 " ideal model delta sigma weight residual 120.20 135.17 -14.97 1.50e+00 4.44e-01 9.96e+01 angle pdb=" O3' DG N 136 " pdb=" C3' DG N 136 " pdb=" C2' DG N 136 " ideal model delta sigma weight residual 111.50 98.40 13.10 1.50e+00 4.44e-01 7.62e+01 angle pdb=" C3' DT T 19 " pdb=" O3' DT T 19 " pdb=" P DT T 20 " ideal model delta sigma weight residual 120.20 107.31 12.89 1.50e+00 4.44e-01 7.38e+01 ... (remaining 16135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.06: 6440 30.06 - 60.11: 443 60.11 - 90.17: 25 90.17 - 120.22: 2 120.22 - 150.28: 4 Dihedral angle restraints: 6914 sinusoidal: 3234 harmonic: 3680 Sorted by residual: dihedral pdb=" O5' GTP C 201 " pdb=" O3A GTP C 201 " pdb=" PA GTP C 201 " pdb=" PB GTP C 201 " ideal model delta sinusoidal sigma weight residual -85.88 55.19 -141.07 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" O3A GTP C 201 " pdb=" O3B GTP C 201 " pdb=" PB GTP C 201 " pdb=" PG GTP C 201 " ideal model delta sinusoidal sigma weight residual 303.79 167.39 136.40 1 2.00e+01 2.50e-03 4.14e+01 dihedral pdb=" C8 GTP C 201 " pdb=" C1' GTP C 201 " pdb=" N9 GTP C 201 " pdb=" O4' GTP C 201 " ideal model delta sinusoidal sigma weight residual 104.59 -18.61 123.20 1 2.00e+01 2.50e-03 3.71e+01 ... (remaining 6911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1716 0.134 - 0.268: 32 0.268 - 0.402: 7 0.402 - 0.536: 25 0.536 - 0.670: 8 Chirality restraints: 1788 Sorted by residual: chirality pdb=" C1' DG T 16 " pdb=" O4' DG T 16 " pdb=" C2' DG T 16 " pdb=" N9 DG T 16 " both_signs ideal model delta sigma weight residual False 2.42 1.75 0.67 2.00e-01 2.50e+01 1.12e+01 chirality pdb=" P DT N 109 " pdb=" OP1 DT N 109 " pdb=" OP2 DT N 109 " pdb=" O5' DT N 109 " both_signs ideal model delta sigma weight residual True 2.35 -2.97 -0.62 2.00e-01 2.50e+01 9.69e+00 chirality pdb=" P DC T 10 " pdb=" OP1 DC T 10 " pdb=" OP2 DC T 10 " pdb=" O5' DC T 10 " both_signs ideal model delta sigma weight residual True 2.35 -2.97 -0.62 2.00e-01 2.50e+01 9.64e+00 ... (remaining 1785 not shown) Planarity restraints: 1841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 900 " -0.056 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO A 901 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 901 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 901 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 767 " 0.057 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO A 768 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 768 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 768 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 462 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 463 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " -0.027 5.00e-02 4.00e+02 ... (remaining 1838 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 34 2.45 - 3.07: 7263 3.07 - 3.68: 17234 3.68 - 4.29: 25192 4.29 - 4.90: 40994 Nonbonded interactions: 90717 Sorted by model distance: nonbonded pdb=" OE1 GLN B 336 " pdb=" N2 DG T 25 " model vdw 1.842 2.520 nonbonded pdb=" O ASN A 900 " pdb=" OD1 ASN A 900 " model vdw 2.082 3.040 nonbonded pdb=" OG1 THR A1132 " pdb=" O GLN A1135 " model vdw 2.223 2.440 nonbonded pdb=" OE1 GLN A 944 " pdb=" OG SER A1351 " model vdw 2.253 2.440 nonbonded pdb=" OG SER A 794 " pdb=" N7 DG T 25 " model vdw 2.267 2.520 ... (remaining 90712 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: 0.080 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: 1.240 Check model and map are aligned: 0.160 Set scattering table: 0.110 Process input model: 39.330 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.060 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:3.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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 : 0.007 0.121 11708 Z= 0.356 Angle : 1.037 22.496 16140 Z= 0.543 Chirality : 0.087 0.670 1788 Planarity : 0.005 0.084 1841 Dihedral : 18.483 150.277 4530 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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: 0.62 (0.24), residues: 1252 helix: 1.71 (0.21), residues: 649 sheet: -0.89 (0.49), residues: 111 loop : -1.04 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 915 HIS 0.004 0.001 HIS A1169 PHE 0.029 0.001 PHE A1338 TYR 0.024 0.001 TYR B 161 ARG 0.004 0.000 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.206 Fit side-chains REVERT: A 476 LEU cc_start: 0.6034 (mt) cc_final: 0.5205 (tt) REVERT: A 1005 LYS cc_start: 0.7467 (tmmt) cc_final: 0.7193 (tttp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2506 time to fit residues: 65.6638 Evaluate side-chains 150 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 117 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 187 HIS A 900 ASN ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11708 Z= 0.284 Angle : 0.597 9.472 16140 Z= 0.314 Chirality : 0.041 0.150 1788 Planarity : 0.005 0.057 1841 Dihedral : 19.973 170.265 2103 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.39 % Favored : 95.45 % Rotamer: Outliers : 2.05 % Allowed : 8.29 % Favored : 89.66 % 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: 0.56 (0.24), residues: 1252 helix: 1.66 (0.21), residues: 655 sheet: -0.85 (0.46), residues: 127 loop : -1.13 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 915 HIS 0.011 0.001 HIS B 187 PHE 0.018 0.001 PHE A1161 TYR 0.025 0.002 TYR B 161 ARG 0.005 0.000 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 151 time to evaluate : 1.220 Fit side-chains REVERT: B 137 ASN cc_start: 0.8927 (OUTLIER) cc_final: 0.8420 (t0) REVERT: B 321 TRP cc_start: 0.7930 (t60) cc_final: 0.6987 (t60) outliers start: 22 outliers final: 14 residues processed: 165 average time/residue: 0.2361 time to fit residues: 56.1789 Evaluate side-chains 159 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 187 HIS Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 475 LEU Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN A 492 ASN A 900 ASN A 987 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11708 Z= 0.247 Angle : 0.573 8.798 16140 Z= 0.299 Chirality : 0.039 0.144 1788 Planarity : 0.005 0.053 1841 Dihedral : 19.486 144.425 2103 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.47 % Favored : 95.37 % Rotamer: Outliers : 2.61 % Allowed : 11.18 % Favored : 86.21 % 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: 0.49 (0.24), residues: 1252 helix: 1.57 (0.21), residues: 665 sheet: -0.92 (0.44), residues: 128 loop : -1.15 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 915 HIS 0.028 0.001 HIS B 187 PHE 0.017 0.001 PHE A1338 TYR 0.025 0.001 TYR B 161 ARG 0.002 0.000 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 152 time to evaluate : 1.248 Fit side-chains REVERT: B 137 ASN cc_start: 0.8955 (OUTLIER) cc_final: 0.8585 (t0) REVERT: B 321 TRP cc_start: 0.7934 (t60) cc_final: 0.7161 (t60) REVERT: A 967 VAL cc_start: 0.9034 (p) cc_final: 0.8755 (p) outliers start: 28 outliers final: 19 residues processed: 166 average time/residue: 0.2277 time to fit residues: 54.9661 Evaluate side-chains 162 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 142 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 10.0000 chunk 88 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 12 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 78 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 124 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN A 900 ASN A 968 ASN A 987 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11708 Z= 0.186 Angle : 0.542 9.950 16140 Z= 0.281 Chirality : 0.038 0.140 1788 Planarity : 0.004 0.052 1841 Dihedral : 19.122 136.334 2103 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 2.33 % Allowed : 13.61 % Favored : 84.06 % 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: 0.52 (0.24), residues: 1252 helix: 1.63 (0.21), residues: 665 sheet: -1.00 (0.43), residues: 128 loop : -1.17 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 915 HIS 0.004 0.001 HIS B 187 PHE 0.016 0.001 PHE A1338 TYR 0.023 0.001 TYR B 161 ARG 0.002 0.000 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 1.286 Fit side-chains REVERT: B 137 ASN cc_start: 0.8857 (OUTLIER) cc_final: 0.8345 (t0) REVERT: B 247 MET cc_start: 0.8358 (mmt) cc_final: 0.7932 (tpp) REVERT: B 319 MET cc_start: 0.8411 (mmm) cc_final: 0.8166 (mmm) REVERT: B 321 TRP cc_start: 0.7842 (t60) cc_final: 0.7220 (t60) REVERT: A 519 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6925 (pp) REVERT: A 967 VAL cc_start: 0.9028 (p) cc_final: 0.8752 (p) REVERT: A 1018 MET cc_start: 0.9060 (tmm) cc_final: 0.8816 (ttp) outliers start: 25 outliers final: 15 residues processed: 168 average time/residue: 0.2477 time to fit residues: 59.4822 Evaluate side-chains 162 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1055 THR Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 106 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN A 900 ASN A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11708 Z= 0.281 Angle : 0.583 9.206 16140 Z= 0.303 Chirality : 0.040 0.145 1788 Planarity : 0.004 0.055 1841 Dihedral : 19.037 136.276 2103 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.79 % Favored : 95.05 % Rotamer: Outliers : 2.89 % Allowed : 14.63 % Favored : 82.48 % 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: 0.43 (0.24), residues: 1252 helix: 1.56 (0.21), residues: 664 sheet: -1.03 (0.43), residues: 129 loop : -1.22 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 915 HIS 0.005 0.001 HIS B 187 PHE 0.018 0.001 PHE A1338 TYR 0.026 0.001 TYR B 161 ARG 0.003 0.000 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 148 time to evaluate : 1.183 Fit side-chains REVERT: B 114 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7500 (mp0) REVERT: B 137 ASN cc_start: 0.8862 (OUTLIER) cc_final: 0.8395 (t0) REVERT: B 247 MET cc_start: 0.8424 (mmt) cc_final: 0.7927 (tpp) REVERT: B 321 TRP cc_start: 0.7988 (t60) cc_final: 0.7486 (t60) REVERT: A 503 ILE cc_start: 0.8005 (OUTLIER) cc_final: 0.7746 (mp) REVERT: A 519 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6953 (pp) outliers start: 31 outliers final: 21 residues processed: 167 average time/residue: 0.2325 time to fit residues: 55.6598 Evaluate side-chains 167 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1055 THR Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 120 optimal weight: 20.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN A 900 ASN A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11708 Z= 0.219 Angle : 0.549 9.233 16140 Z= 0.286 Chirality : 0.038 0.140 1788 Planarity : 0.004 0.054 1841 Dihedral : 18.949 135.780 2103 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.31 % Favored : 95.53 % Rotamer: Outliers : 2.98 % Allowed : 14.63 % Favored : 82.39 % 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: 0.46 (0.24), residues: 1252 helix: 1.59 (0.21), residues: 665 sheet: -0.96 (0.43), residues: 128 loop : -1.22 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 915 HIS 0.005 0.001 HIS B 187 PHE 0.019 0.001 PHE A1338 TYR 0.025 0.001 TYR B 161 ARG 0.003 0.000 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.216 Fit side-chains REVERT: B 114 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: B 137 ASN cc_start: 0.8785 (OUTLIER) cc_final: 0.8239 (t0) REVERT: B 247 MET cc_start: 0.8412 (mmt) cc_final: 0.7892 (tpp) REVERT: B 321 TRP cc_start: 0.7964 (t60) cc_final: 0.7504 (t60) REVERT: A 503 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7727 (mp) REVERT: A 519 LEU cc_start: 0.7372 (OUTLIER) cc_final: 0.6793 (pp) outliers start: 32 outliers final: 21 residues processed: 174 average time/residue: 0.2330 time to fit residues: 58.3686 Evaluate side-chains 172 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 147 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1055 THR Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 70 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 57 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN A 900 ASN A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11708 Z= 0.277 Angle : 0.580 9.125 16140 Z= 0.302 Chirality : 0.040 0.142 1788 Planarity : 0.004 0.055 1841 Dihedral : 18.965 135.714 2103 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.87 % Favored : 94.97 % Rotamer: Outliers : 3.17 % Allowed : 15.66 % Favored : 81.17 % 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: 0.37 (0.24), residues: 1252 helix: 1.53 (0.21), residues: 665 sheet: -0.98 (0.42), residues: 128 loop : -1.31 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 915 HIS 0.005 0.001 HIS B 187 PHE 0.017 0.001 PHE A1338 TYR 0.023 0.001 TYR B 161 ARG 0.003 0.000 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 1.134 Fit side-chains REVERT: B 114 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: B 137 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8114 (t0) REVERT: B 247 MET cc_start: 0.8471 (mmt) cc_final: 0.7961 (tpp) REVERT: B 321 TRP cc_start: 0.8001 (t60) cc_final: 0.7569 (t60) REVERT: A 519 LEU cc_start: 0.7359 (OUTLIER) cc_final: 0.6935 (pp) outliers start: 34 outliers final: 22 residues processed: 177 average time/residue: 0.2342 time to fit residues: 59.6391 Evaluate side-chains 173 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 148 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1055 THR Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 119 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN A 900 ASN A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11708 Z= 0.292 Angle : 0.594 9.045 16140 Z= 0.309 Chirality : 0.040 0.159 1788 Planarity : 0.004 0.055 1841 Dihedral : 18.985 135.706 2103 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.27 % Favored : 94.57 % Rotamer: Outliers : 3.17 % Allowed : 15.66 % Favored : 81.17 % 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: 0.33 (0.24), residues: 1252 helix: 1.51 (0.21), residues: 661 sheet: -1.06 (0.42), residues: 129 loop : -1.30 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 915 HIS 0.005 0.001 HIS B 187 PHE 0.022 0.001 PHE A1338 TYR 0.028 0.002 TYR B 161 ARG 0.003 0.000 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 152 time to evaluate : 1.409 Fit side-chains REVERT: B 114 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: B 137 ASN cc_start: 0.8855 (OUTLIER) cc_final: 0.8483 (t0) REVERT: B 319 MET cc_start: 0.8388 (mmm) cc_final: 0.7965 (mmm) REVERT: B 321 TRP cc_start: 0.8008 (t60) cc_final: 0.7576 (t60) REVERT: A 519 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7005 (pp) REVERT: A 926 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6824 (mp0) REVERT: A 1215 VAL cc_start: 0.7394 (OUTLIER) cc_final: 0.7166 (t) outliers start: 34 outliers final: 24 residues processed: 175 average time/residue: 0.2359 time to fit residues: 59.1797 Evaluate side-chains 176 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 147 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1019 THR Chi-restraints excluded: chain A residue 1055 THR Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 10.0000 chunk 115 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 109 optimal weight: 0.0670 chunk 76 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN A 900 ASN A 987 GLN A1129 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11708 Z= 0.286 Angle : 0.594 8.960 16140 Z= 0.308 Chirality : 0.040 0.146 1788 Planarity : 0.004 0.055 1841 Dihedral : 18.988 135.703 2103 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.35 % Favored : 94.49 % Rotamer: Outliers : 3.36 % Allowed : 15.84 % Favored : 80.80 % 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: 0.25 (0.24), residues: 1252 helix: 1.43 (0.21), residues: 668 sheet: -1.09 (0.42), residues: 129 loop : -1.36 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 915 HIS 0.005 0.001 HIS B 187 PHE 0.021 0.001 PHE A1338 TYR 0.028 0.002 TYR B 161 ARG 0.003 0.000 ARG B 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 1.209 Fit side-chains REVERT: B 114 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: B 137 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8135 (t0) REVERT: B 319 MET cc_start: 0.8355 (mmm) cc_final: 0.7942 (mmm) REVERT: B 321 TRP cc_start: 0.8006 (t60) cc_final: 0.7588 (t60) REVERT: A 519 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.6981 (pp) REVERT: A 926 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: A 1051 SER cc_start: 0.8162 (t) cc_final: 0.7747 (p) REVERT: A 1215 VAL cc_start: 0.7424 (OUTLIER) cc_final: 0.7198 (t) outliers start: 36 outliers final: 25 residues processed: 174 average time/residue: 0.2413 time to fit residues: 60.5245 Evaluate side-chains 176 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 700 THR Chi-restraints excluded: chain A residue 755 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1055 THR Chi-restraints excluded: chain A residue 1065 LEU Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 1.9990 chunk 58 optimal weight: 0.0020 chunk 85 optimal weight: 2.9990 chunk 128 optimal weight: 10.0000 chunk 118 optimal weight: 9.9990 chunk 102 optimal weight: 0.5980 chunk 10 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 overall best weight: 1.9194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 287 GLN A 900 ASN A 987 GLN A1129 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11708 Z= 0.178 Angle : 0.550 8.906 16140 Z= 0.284 Chirality : 0.038 0.139 1788 Planarity : 0.004 0.052 1841 Dihedral : 18.855 134.878 2103 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.61 % Allowed : 16.87 % Favored : 80.52 % 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: 0.36 (0.24), residues: 1252 helix: 1.53 (0.21), residues: 672 sheet: -1.05 (0.42), residues: 124 loop : -1.35 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 915 HIS 0.004 0.001 HIS B 187 PHE 0.020 0.001 PHE A1338 TYR 0.029 0.001 TYR B 161 ARG 0.004 0.000 ARG B 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 158 time to evaluate : 1.255 Fit side-chains REVERT: B 8 ILE cc_start: 0.7459 (tp) cc_final: 0.7142 (tp) REVERT: B 247 MET cc_start: 0.8454 (mmt) cc_final: 0.7901 (tpp) REVERT: B 319 MET cc_start: 0.8328 (mmm) cc_final: 0.8039 (mmm) REVERT: B 321 TRP cc_start: 0.7978 (t60) cc_final: 0.7545 (t60) REVERT: A 519 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.6885 (pp) REVERT: A 926 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: A 1051 SER cc_start: 0.8099 (t) cc_final: 0.7694 (p) REVERT: A 1215 VAL cc_start: 0.7472 (OUTLIER) cc_final: 0.7243 (t) outliers start: 28 outliers final: 18 residues processed: 175 average time/residue: 0.2385 time to fit residues: 59.7852 Evaluate side-chains 174 residues out of total 1125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 153 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1055 THR Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1200 THR Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 20.0000 chunk 94 optimal weight: 4.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 8.9990 chunk 102 optimal weight: 0.9980 chunk 42 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 287 GLN A 900 ASN A 987 GLN A1129 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.155919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.128970 restraints weight = 15420.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.130037 restraints weight = 12739.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.131229 restraints weight = 11090.463| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11708 Z= 0.241 Angle : 0.568 8.659 16140 Z= 0.294 Chirality : 0.039 0.143 1788 Planarity : 0.004 0.053 1841 Dihedral : 18.877 135.032 2103 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.11 % Favored : 94.73 % Rotamer: Outliers : 2.42 % Allowed : 17.33 % Favored : 80.24 % 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: 0.34 (0.24), residues: 1252 helix: 1.51 (0.21), residues: 670 sheet: -1.08 (0.43), residues: 125 loop : -1.32 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 915 HIS 0.005 0.001 HIS B 187 PHE 0.020 0.001 PHE A1338 TYR 0.029 0.001 TYR B 161 ARG 0.003 0.000 ARG B 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1975.69 seconds wall clock time: 37 minutes 9.56 seconds (2229.56 seconds total)