Starting phenix.real_space_refine on Wed Jun 18 11:05:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yny_39431/06_2025/8yny_39431.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yny_39431/06_2025/8yny_39431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yny_39431/06_2025/8yny_39431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yny_39431/06_2025/8yny_39431.map" model { file = "/net/cci-nas-00/data/ceres_data/8yny_39431/06_2025/8yny_39431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yny_39431/06_2025/8yny_39431.cif" } resolution = 4.52 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= 0.003 sd= 0.094 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 386 5.49 5 S 30 5.16 5 C 12247 2.51 5 N 3895 2.21 5 O 4829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21387 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 743 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "D" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "E" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 738 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "F" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "G" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "H" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "I" Number of atoms: 2794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 2794 Classifications: {'DNA': 137} Link IDs: {'rna3p': 136} Chain: "J" Number of atoms: 2783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 2783 Classifications: {'DNA': 135} Link IDs: {'rna3p': 134} Chain: "K" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 351 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "W" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 2072 Classifications: {'RNA': 97} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 48, 'rna3p_pyr': 38} Link IDs: {'rna2p': 11, 'rna3p': 85} Chain: "X" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 941, 7759 Classifications: {'peptide': 941} Link IDs: {'PTRANS': 26, 'TRANS': 914} Chain breaks: 13 Time building chain proxies: 12.03, per 1000 atoms: 0.56 Number of scatterers: 21387 At special positions: 0 Unit cell: (106.575, 115.71, 190.312, 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 30 16.00 P 386 15.00 O 4829 8.00 N 3895 7.00 C 12247 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 - 3.00 Amino acid : True - 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: 4.87 Conformation dependent library (CDL) restraints added in 2.1 seconds 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3126 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 8 sheets defined 64.7% alpha, 5.1% beta 167 base pairs and 277 stacking pairs defined. Time for finding SS restraints: 8.81 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.660A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 79 removed outlier: 3.901A pdb=" N LEU A 70 " --> pdb=" O PRO A 66 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.527A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 47 through 76 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.290A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.915A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 88 through 99 Processing helix chain 'D' and resid 103 through 121 Processing helix chain 'E' and resid 47 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.791A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.980A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ALA E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N HIS E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.544A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.619A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 47 through 77 removed outlier: 3.798A pdb=" N TYR F 51 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU F 52 " --> pdb=" O GLY F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 38 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.042A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 4.105A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN G 84 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 98 removed outlier: 3.681A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 82 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.772A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'X' and resid 59 through 91 removed outlier: 4.512A pdb=" N ASN X 88 " --> pdb=" O GLU X 84 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N GLU X 89 " --> pdb=" O ILE X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 95 through 104 removed outlier: 3.733A pdb=" N HIS X 99 " --> pdb=" O ASP X 95 " (cutoff:3.500A) Processing helix chain 'X' and resid 121 through 132 removed outlier: 3.552A pdb=" N GLU X 125 " --> pdb=" O ASN X 121 " (cutoff:3.500A) Processing helix chain 'X' and resid 134 through 145 removed outlier: 3.795A pdb=" N LEU X 138 " --> pdb=" O THR X 134 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 164 Processing helix chain 'X' and resid 315 through 343 removed outlier: 3.789A pdb=" N ALA X 319 " --> pdb=" O ALA X 315 " (cutoff:3.500A) Processing helix chain 'X' and resid 343 through 353 removed outlier: 3.819A pdb=" N ASP X 353 " --> pdb=" O GLU X 349 " (cutoff:3.500A) Processing helix chain 'X' and resid 358 through 364 Processing helix chain 'X' and resid 368 through 383 Proline residue: X 378 - end of helix Processing helix chain 'X' and resid 387 through 395 Processing helix chain 'X' and resid 405 through 410 removed outlier: 4.158A pdb=" N GLY X 408 " --> pdb=" O PHE X 405 " (cutoff:3.500A) Processing helix chain 'X' and resid 411 through 427 removed outlier: 4.204A pdb=" N HIS X 415 " --> pdb=" O PRO X 411 " (cutoff:3.500A) Processing helix chain 'X' and resid 430 through 436 Processing helix chain 'X' and resid 436 through 446 Processing helix chain 'X' and resid 477 through 482 Processing helix chain 'X' and resid 483 through 494 Processing helix chain 'X' and resid 512 through 525 Processing helix chain 'X' and resid 591 through 598 Processing helix chain 'X' and resid 614 through 626 Processing helix chain 'X' and resid 628 through 637 Processing helix chain 'X' and resid 644 through 654 Processing helix chain 'X' and resid 663 through 668 Processing helix chain 'X' and resid 679 through 685 Processing helix chain 'X' and resid 692 through 698 Processing helix chain 'X' and resid 702 through 709 removed outlier: 4.070A pdb=" N GLU X 706 " --> pdb=" O LEU X 702 " (cutoff:3.500A) Processing helix chain 'X' and resid 720 through 727 Processing helix chain 'X' and resid 730 through 751 Processing helix chain 'X' and resid 926 through 940 Processing helix chain 'X' and resid 959 through 971 removed outlier: 3.637A pdb=" N VAL X 963 " --> pdb=" O LYS X 959 " (cutoff:3.500A) Processing helix chain 'X' and resid 980 through 999 removed outlier: 3.701A pdb=" N ALA X 987 " --> pdb=" O HIS X 983 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR X 988 " --> pdb=" O ALA X 984 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY X 994 " --> pdb=" O ASN X 990 " (cutoff:3.500A) Processing helix chain 'X' and resid 1001 through 1007 Processing helix chain 'X' and resid 1041 through 1047 removed outlier: 4.248A pdb=" N PHE X1045 " --> pdb=" O ILE X1042 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS X1047 " --> pdb=" O ASN X1044 " (cutoff:3.500A) Processing helix chain 'X' and resid 1077 through 1089 Processing helix chain 'X' and resid 1127 through 1132 Processing helix chain 'X' and resid 1168 through 1177 removed outlier: 4.160A pdb=" N SER X1172 " --> pdb=" O ILE X1168 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER X1173 " --> pdb=" O MET X1169 " (cutoff:3.500A) Processing helix chain 'X' and resid 1177 through 1185 Processing helix chain 'X' and resid 1191 through 1195 Processing helix chain 'X' and resid 1229 through 1241 Processing helix chain 'X' and resid 1254 through 1262 Processing helix chain 'X' and resid 1262 through 1281 Processing helix chain 'X' and resid 1283 through 1298 removed outlier: 3.617A pdb=" N LEU X1287 " --> pdb=" O ALA X1283 " (cutoff:3.500A) Processing helix chain 'X' and resid 1301 through 1313 Processing helix chain 'X' and resid 1314 through 1316 No H-bonds generated for 'chain 'X' and resid 1314 through 1316' Processing helix chain 'X' and resid 1339 through 1345 removed outlier: 3.678A pdb=" N ASP X1344 " --> pdb=" O LYS X1340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.982A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA3, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'X' and resid 954 through 957 removed outlier: 4.168A pdb=" N ASN X 758 " --> pdb=" O TYR X 5 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 29 through 33 Processing sheet with id=AA6, first strand: chain 'X' and resid 1156 through 1167 removed outlier: 5.704A pdb=" N LYS X1156 " --> pdb=" O GLU X1150 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLU X1150 " --> pdb=" O LYS X1156 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LYS X1158 " --> pdb=" O LYS X1148 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LYS X1148 " --> pdb=" O LYS X1158 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL X1160 " --> pdb=" O VAL X1146 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N VAL X1146 " --> pdb=" O VAL X1160 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLU X1162 " --> pdb=" O LEU X1144 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU X1144 " --> pdb=" O GLU X1162 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU X1164 " --> pdb=" O SER X1142 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N SER X1142 " --> pdb=" O LEU X1164 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE X1166 " --> pdb=" O ALA X1140 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE X1196 " --> pdb=" O LEU X1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'X' and resid 1220 through 1222 removed outlier: 3.841A pdb=" N SER X1202 " --> pdb=" O LEU X1214 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU X1203 " --> pdb=" O ILE X1348 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE X1348 " --> pdb=" O LEU X1203 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLU X1205 " --> pdb=" O THR X1346 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR X1346 " --> pdb=" O GLU X1205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'X' and resid 1324 through 1325 761 hydrogen bonds defined for protein. 2256 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 431 hydrogen bonds 854 hydrogen bond angles 0 basepair planarities 167 basepair parallelities 277 stacking parallelities Total time for adding SS restraints: 13.20 Time building geometry restraints manager: 5.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4252 1.33 - 1.45: 6775 1.45 - 1.57: 10716 1.57 - 1.69: 768 1.69 - 1.81: 55 Bond restraints: 22566 Sorted by residual: bond pdb=" N ILE D 86 " pdb=" CA ILE D 86 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.22e-02 6.72e+03 7.84e+00 bond pdb=" P DG I 28 " pdb=" OP2 DG I 28 " ideal model delta sigma weight residual 1.480 1.523 -0.043 2.00e-02 2.50e+03 4.67e+00 bond pdb=" P DG J 21 " pdb=" OP1 DG J 21 " ideal model delta sigma weight residual 1.480 1.522 -0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" P DC I 9 " pdb=" OP2 DC I 9 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.30e+00 bond pdb=" P DC J 67 " pdb=" OP2 DC J 67 " ideal model delta sigma weight residual 1.480 1.521 -0.041 2.00e-02 2.50e+03 4.28e+00 ... (remaining 22561 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 31364 2.25 - 4.51: 616 4.51 - 6.76: 123 6.76 - 9.01: 26 9.01 - 11.26: 4 Bond angle restraints: 32133 Sorted by residual: angle pdb=" O3' DT I 17 " pdb=" P DC I 18 " pdb=" O5' DC I 18 " ideal model delta sigma weight residual 104.00 95.46 8.54 1.50e+00 4.44e-01 3.24e+01 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" O5' DG J 21 " ideal model delta sigma weight residual 104.00 96.07 7.93 1.50e+00 4.44e-01 2.80e+01 angle pdb=" O3' DC I 18 " pdb=" P DC I 19 " pdb=" O5' DC I 19 " ideal model delta sigma weight residual 104.00 97.07 6.93 1.50e+00 4.44e-01 2.13e+01 angle pdb=" O3' DC I 19 " pdb=" P DG I 20 " pdb=" O5' DG I 20 " ideal model delta sigma weight residual 104.00 97.43 6.57 1.50e+00 4.44e-01 1.92e+01 angle pdb=" O3' DC I 30 " pdb=" P DC I 31 " pdb=" O5' DC I 31 " ideal model delta sigma weight residual 104.00 97.47 6.53 1.50e+00 4.44e-01 1.90e+01 ... (remaining 32128 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.57: 10809 31.57 - 63.13: 1977 63.13 - 94.70: 143 94.70 - 126.27: 11 126.27 - 157.84: 4 Dihedral angle restraints: 12944 sinusoidal: 8120 harmonic: 4824 Sorted by residual: dihedral pdb=" CA TYR F 98 " pdb=" C TYR F 98 " pdb=" N GLY F 99 " pdb=" CA GLY F 99 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" C4' A W 28 " pdb=" O4' A W 28 " pdb=" C1' A W 28 " pdb=" C2' A W 28 " ideal model delta sinusoidal sigma weight residual -21.00 7.49 -28.49 1 8.00e+00 1.56e-02 1.82e+01 dihedral pdb=" C3' A W 28 " pdb=" C4' A W 28 " pdb=" O4' A W 28 " pdb=" C1' A W 28 " ideal model delta sinusoidal sigma weight residual -2.00 -28.60 26.60 1 8.00e+00 1.56e-02 1.59e+01 ... (remaining 12941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 3630 0.122 - 0.244: 23 0.244 - 0.366: 0 0.366 - 0.488: 4 0.488 - 0.610: 45 Chirality restraints: 3702 Sorted by residual: chirality pdb=" P DG I 28 " pdb=" OP1 DG I 28 " pdb=" OP2 DG I 28 " pdb=" O5' DG I 28 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.61 2.00e-01 2.50e+01 9.30e+00 chirality pdb=" P DG I 47 " pdb=" OP1 DG I 47 " pdb=" OP2 DG I 47 " pdb=" O5' DG I 47 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.61 2.00e-01 2.50e+01 9.26e+00 chirality pdb=" P DT J 68 " pdb=" OP1 DT J 68 " pdb=" OP2 DT J 68 " pdb=" O5' DT J 68 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.61 2.00e-01 2.50e+01 9.20e+00 ... (remaining 3699 not shown) Planarity restraints: 2702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 100 " 0.006 2.00e-02 2.50e+03 2.71e-02 1.65e+01 pdb=" N1 DC I 100 " -0.010 2.00e-02 2.50e+03 pdb=" C2 DC I 100 " 0.068 2.00e-02 2.50e+03 pdb=" O2 DC I 100 " -0.033 2.00e-02 2.50e+03 pdb=" N3 DC I 100 " -0.023 2.00e-02 2.50e+03 pdb=" C4 DC I 100 " 0.000 2.00e-02 2.50e+03 pdb=" N4 DC I 100 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 100 " -0.010 2.00e-02 2.50e+03 pdb=" C6 DC I 100 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J -18 " -0.020 2.00e-02 2.50e+03 1.57e-02 7.37e+00 pdb=" N9 DG J -18 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG J -18 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DG J -18 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG J -18 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG J -18 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG J -18 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG J -18 " 0.012 2.00e-02 2.50e+03 pdb=" C2 DG J -18 " -0.035 2.00e-02 2.50e+03 pdb=" N2 DG J -18 " 0.023 2.00e-02 2.50e+03 pdb=" N3 DG J -18 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DG J -18 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 38 " -0.034 2.00e-02 2.50e+03 1.53e-02 7.03e+00 pdb=" N9 DG J 38 " 0.038 2.00e-02 2.50e+03 pdb=" C8 DG J 38 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DG J 38 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DG J 38 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DG J 38 " -0.008 2.00e-02 2.50e+03 pdb=" O6 DG J 38 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DG J 38 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG J 38 " 0.005 2.00e-02 2.50e+03 pdb=" N2 DG J 38 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DG J 38 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DG J 38 " -0.003 2.00e-02 2.50e+03 ... (remaining 2699 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 2067 2.74 - 3.28: 23061 3.28 - 3.82: 43980 3.82 - 4.36: 50281 4.36 - 4.90: 70903 Nonbonded interactions: 190292 Sorted by model distance: nonbonded pdb=" O2' C W 8 " pdb=" OP1 C W 9 " model vdw 2.194 3.040 nonbonded pdb=" O2' A W 42 " pdb=" OP1 G W 43 " model vdw 2.202 3.040 nonbonded pdb=" NH1 ARG E 116 " pdb=" OP2 DC J -2 " model vdw 2.207 3.120 nonbonded pdb=" O ALA X 149 " pdb=" OH TYR X 430 " model vdw 2.211 3.040 nonbonded pdb=" OP1 G W 16 " pdb=" NH2 ARG X 74 " model vdw 2.213 3.120 ... (remaining 190287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 46 through 134) selection = (chain 'E' and resid 46 through 134) } ncs_group { reference = (chain 'B' and resid 25 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 109) selection = (chain 'G' and resid 16 through 109) } ncs_group { reference = chain 'D' selection = chain 'H' } 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: 0.530 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: 0.020 Extract box with map and model: 0.720 Check model and map are aligned: 0.150 Set scattering table: 0.250 Process input model: 57.360 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 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 0.051 22566 Z= 0.234 Angle : 0.815 11.263 32133 Z= 0.440 Chirality : 0.073 0.610 3702 Planarity : 0.004 0.043 2702 Dihedral : 25.386 157.836 9818 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 24.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.14 % Allowed : 7.49 % Favored : 92.37 % 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: 0.54 (0.20), residues: 1609 helix: 1.07 (0.16), residues: 942 sheet: 0.09 (0.59), residues: 75 loop : -0.67 (0.25), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 464 HIS 0.006 0.001 HIS F 75 PHE 0.013 0.002 PHE X1313 TYR 0.016 0.002 TYR C 57 ARG 0.006 0.001 ARG X1210 Details of bonding type rmsd hydrogen bonds : bond 0.13676 ( 1192) hydrogen bonds : angle 6.24768 ( 3110) covalent geometry : bond 0.00488 (22566) covalent geometry : angle 0.81519 (32133) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 1.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 99 average time/residue: 0.3616 time to fit residues: 55.2575 Evaluate side-chains 53 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 168 optimal weight: 7.9990 chunk 150 optimal weight: 4.9990 chunk 83 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 24 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 14 ASN X 129 HIS X 415 HIS X 459 ASN ** X 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X1234 ASN X1256 GLN ** X1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.034365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.028143 restraints weight = 380713.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.028706 restraints weight = 253045.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.029059 restraints weight = 191204.008| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22566 Z= 0.261 Angle : 0.719 10.837 32133 Z= 0.405 Chirality : 0.041 0.238 3702 Planarity : 0.005 0.059 2702 Dihedral : 29.651 174.551 6426 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 23.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.14 % Allowed : 3.96 % Favored : 95.91 % 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: 0.70 (0.20), residues: 1609 helix: 1.17 (0.16), residues: 1021 sheet: -0.48 (0.50), residues: 90 loop : -0.73 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP X 464 HIS 0.006 0.002 HIS F 75 PHE 0.018 0.002 PHE X 626 TYR 0.019 0.002 TYR X1232 ARG 0.008 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.08508 ( 1192) hydrogen bonds : angle 4.54746 ( 3110) covalent geometry : bond 0.00547 (22566) covalent geometry : angle 0.71910 (32133) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 1.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9174 (t80) cc_final: 0.8770 (t80) REVERT: A 90 MET cc_start: 0.9435 (mmp) cc_final: 0.9174 (mmm) REVERT: D 105 LYS cc_start: 0.9554 (pttm) cc_final: 0.9329 (mptt) REVERT: D 106 HIS cc_start: 0.9582 (m90) cc_final: 0.9330 (m90) REVERT: H 59 MET cc_start: 0.9743 (mmm) cc_final: 0.9493 (mmm) REVERT: H 68 GLU cc_start: 0.9261 (tt0) cc_final: 0.9012 (tm-30) REVERT: H 77 LEU cc_start: 0.9731 (tt) cc_final: 0.9527 (pp) REVERT: H 79 HIS cc_start: 0.9537 (m90) cc_final: 0.9197 (m90) REVERT: X 751 MET cc_start: 0.9184 (ttm) cc_final: 0.8940 (ttp) REVERT: X 1169 MET cc_start: 0.9608 (ttm) cc_final: 0.9085 (tpp) outliers start: 2 outliers final: 0 residues processed: 70 average time/residue: 0.3419 time to fit residues: 38.8818 Evaluate side-chains 53 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 181 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 158 optimal weight: 30.0000 chunk 1 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 723 HIS ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X1308 ASN ** X1317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.033369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.027212 restraints weight = 386728.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.027755 restraints weight = 255273.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.028104 restraints weight = 192619.877| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 22566 Z= 0.248 Angle : 0.666 9.841 32133 Z= 0.380 Chirality : 0.039 0.209 3702 Planarity : 0.005 0.055 2702 Dihedral : 29.768 168.157 6426 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.27 % Rotamer: Outliers : 0.07 % Allowed : 3.61 % Favored : 96.32 % 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: 0.82 (0.20), residues: 1609 helix: 1.32 (0.16), residues: 1009 sheet: -0.92 (0.53), residues: 86 loop : -0.64 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 464 HIS 0.006 0.001 HIS F 75 PHE 0.013 0.002 PHE X 462 TYR 0.019 0.002 TYR X 430 ARG 0.006 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.07784 ( 1192) hydrogen bonds : angle 4.39085 ( 3110) covalent geometry : bond 0.00507 (22566) covalent geometry : angle 0.66560 (32133) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 1.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9272 (t80) cc_final: 0.8886 (t80) REVERT: A 90 MET cc_start: 0.9404 (mmp) cc_final: 0.9078 (mmp) REVERT: D 68 GLU cc_start: 0.9611 (mm-30) cc_final: 0.9339 (mm-30) REVERT: D 106 HIS cc_start: 0.9620 (m90) cc_final: 0.9326 (m90) REVERT: G 102 ILE cc_start: 0.7456 (mp) cc_final: 0.7126 (tt) REVERT: H 68 GLU cc_start: 0.9248 (tt0) cc_final: 0.9015 (tm-30) REVERT: H 77 LEU cc_start: 0.9676 (tt) cc_final: 0.9378 (pp) REVERT: X 419 LEU cc_start: 0.9701 (tt) cc_final: 0.9490 (mt) outliers start: 1 outliers final: 0 residues processed: 63 average time/residue: 0.3360 time to fit residues: 35.1597 Evaluate side-chains 49 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 94 optimal weight: 8.9990 chunk 0 optimal weight: 40.0000 chunk 37 optimal weight: 7.9990 chunk 168 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 181 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 113 optimal weight: 0.0010 chunk 4 optimal weight: 5.9990 overall best weight: 3.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 692 ASN ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X1311 HIS X1317 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.034389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.028052 restraints weight = 380192.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.028614 restraints weight = 247947.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.028984 restraints weight = 186461.074| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22566 Z= 0.164 Angle : 0.597 6.487 32133 Z= 0.340 Chirality : 0.037 0.201 3702 Planarity : 0.004 0.057 2702 Dihedral : 29.394 176.991 6426 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: 1.23 (0.21), residues: 1609 helix: 1.68 (0.16), residues: 1009 sheet: -1.01 (0.50), residues: 94 loop : -0.52 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP X 464 HIS 0.006 0.001 HIS F 75 PHE 0.010 0.001 PHE X 462 TYR 0.015 0.002 TYR G 39 ARG 0.004 0.000 ARG X1210 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 1192) hydrogen bonds : angle 4.00986 ( 3110) covalent geometry : bond 0.00344 (22566) covalent geometry : angle 0.59676 (32133) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 2.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9185 (t80) cc_final: 0.8952 (t80) REVERT: E 92 LEU cc_start: 0.9767 (mm) cc_final: 0.9548 (mt) REVERT: G 102 ILE cc_start: 0.7248 (mp) cc_final: 0.6814 (tt) REVERT: H 68 GLU cc_start: 0.9194 (tt0) cc_final: 0.8990 (tm-30) REVERT: H 77 LEU cc_start: 0.9673 (tt) cc_final: 0.9338 (pp) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.3460 time to fit residues: 36.6750 Evaluate side-chains 52 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 64 optimal weight: 8.9990 chunk 180 optimal weight: 0.0670 chunk 41 optimal weight: 20.0000 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 162 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 119 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 overall best weight: 5.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.033167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.026966 restraints weight = 391883.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.027546 restraints weight = 258342.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.027892 restraints weight = 192000.887| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 22566 Z= 0.211 Angle : 0.625 8.414 32133 Z= 0.355 Chirality : 0.037 0.222 3702 Planarity : 0.004 0.059 2702 Dihedral : 29.528 177.347 6426 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 20.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: 1.16 (0.21), residues: 1609 helix: 1.59 (0.16), residues: 1012 sheet: -1.28 (0.52), residues: 92 loop : -0.43 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP X 464 HIS 0.005 0.001 HIS F 75 PHE 0.014 0.002 PHE E 67 TYR 0.015 0.002 TYR D 34 ARG 0.011 0.000 ARG F 92 Details of bonding type rmsd hydrogen bonds : bond 0.06921 ( 1192) hydrogen bonds : angle 4.23493 ( 3110) covalent geometry : bond 0.00442 (22566) covalent geometry : angle 0.62493 (32133) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 1.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9214 (t80) cc_final: 0.8852 (t80) REVERT: A 90 MET cc_start: 0.9406 (mmp) cc_final: 0.9075 (mmm) REVERT: D 106 HIS cc_start: 0.9688 (m90) cc_final: 0.9465 (m90) REVERT: E 67 PHE cc_start: 0.9321 (t80) cc_final: 0.9115 (t80) REVERT: G 102 ILE cc_start: 0.7456 (mp) cc_final: 0.7064 (tt) REVERT: H 68 GLU cc_start: 0.9178 (tt0) cc_final: 0.8966 (tm-30) REVERT: H 77 LEU cc_start: 0.9569 (tt) cc_final: 0.9285 (pp) REVERT: X 751 MET cc_start: 0.9054 (ttm) cc_final: 0.8538 (ttm) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.3214 time to fit residues: 31.5190 Evaluate side-chains 51 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 96 optimal weight: 30.0000 chunk 189 optimal weight: 10.0000 chunk 178 optimal weight: 30.0000 chunk 185 optimal weight: 10.0000 chunk 195 optimal weight: 0.9980 chunk 184 optimal weight: 0.0270 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 overall best weight: 3.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 402 GLN X 412 HIS ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.034028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.027685 restraints weight = 376886.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.028275 restraints weight = 244743.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.028648 restraints weight = 182056.541| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22566 Z= 0.159 Angle : 0.588 8.523 32133 Z= 0.334 Chirality : 0.036 0.210 3702 Planarity : 0.004 0.065 2702 Dihedral : 29.266 178.287 6426 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: 1.36 (0.21), residues: 1609 helix: 1.77 (0.16), residues: 1007 sheet: -1.09 (0.54), residues: 92 loop : -0.38 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP X1074 HIS 0.005 0.001 HIS F 75 PHE 0.015 0.001 PHE D 62 TYR 0.016 0.001 TYR D 80 ARG 0.010 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.04805 ( 1192) hydrogen bonds : angle 3.98988 ( 3110) covalent geometry : bond 0.00336 (22566) covalent geometry : angle 0.58760 (32133) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9161 (t80) cc_final: 0.8754 (t80) REVERT: A 90 MET cc_start: 0.9384 (mmp) cc_final: 0.9066 (mmm) REVERT: D 106 HIS cc_start: 0.9666 (m90) cc_final: 0.9415 (m90) REVERT: G 102 ILE cc_start: 0.6812 (mp) cc_final: 0.6243 (tt) REVERT: H 77 LEU cc_start: 0.9772 (tt) cc_final: 0.9530 (pp) REVERT: H 79 HIS cc_start: 0.9451 (m90) cc_final: 0.9112 (m90) REVERT: X 90 MET cc_start: 0.9448 (tmm) cc_final: 0.9233 (tmm) REVERT: X 751 MET cc_start: 0.9259 (ttm) cc_final: 0.8836 (ttm) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.3130 time to fit residues: 32.9618 Evaluate side-chains 49 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 110 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 68 optimal weight: 20.0000 chunk 82 optimal weight: 30.0000 chunk 189 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 191 optimal weight: 2.9990 chunk 184 optimal weight: 20.0000 overall best weight: 5.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.032824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.026610 restraints weight = 389629.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.027183 restraints weight = 255879.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.027528 restraints weight = 190024.683| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 22566 Z= 0.216 Angle : 0.627 9.213 32133 Z= 0.356 Chirality : 0.037 0.226 3702 Planarity : 0.004 0.060 2702 Dihedral : 29.524 179.105 6426 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.73 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % 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: 1.27 (0.21), residues: 1609 helix: 1.69 (0.16), residues: 1004 sheet: -1.26 (0.57), residues: 81 loop : -0.41 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP X 464 HIS 0.005 0.001 HIS F 75 PHE 0.018 0.002 PHE C 25 TYR 0.016 0.002 TYR G 39 ARG 0.010 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.06892 ( 1192) hydrogen bonds : angle 4.21653 ( 3110) covalent geometry : bond 0.00451 (22566) covalent geometry : angle 0.62659 (32133) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9261 (t80) cc_final: 0.8864 (t80) REVERT: A 90 MET cc_start: 0.9365 (mmp) cc_final: 0.9035 (mmp) REVERT: D 106 HIS cc_start: 0.9666 (m90) cc_final: 0.9409 (m90) REVERT: E 67 PHE cc_start: 0.9355 (t80) cc_final: 0.9149 (t80) REVERT: G 102 ILE cc_start: 0.7098 (mp) cc_final: 0.6649 (tt) REVERT: H 77 LEU cc_start: 0.9760 (tt) cc_final: 0.9529 (pp) REVERT: H 79 HIS cc_start: 0.9435 (m90) cc_final: 0.9099 (m90) REVERT: X 90 MET cc_start: 0.9388 (tmm) cc_final: 0.9170 (tmm) REVERT: X 751 MET cc_start: 0.9018 (ttm) cc_final: 0.8510 (ttm) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.3350 time to fit residues: 33.9490 Evaluate side-chains 47 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 61 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 88 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 chunk 142 optimal weight: 0.0970 chunk 0 optimal weight: 40.0000 chunk 81 optimal weight: 30.0000 chunk 166 optimal weight: 8.9990 chunk 110 optimal weight: 9.9990 overall best weight: 5.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 GLN ** X 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.032661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.026417 restraints weight = 391002.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.027020 restraints weight = 254537.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.027383 restraints weight = 188098.859| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 22566 Z= 0.213 Angle : 0.630 10.521 32133 Z= 0.358 Chirality : 0.037 0.219 3702 Planarity : 0.004 0.062 2702 Dihedral : 29.601 179.483 6426 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.61 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % 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: 1.09 (0.21), residues: 1609 helix: 1.52 (0.16), residues: 1007 sheet: -1.14 (0.55), residues: 89 loop : -0.42 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP X 659 HIS 0.006 0.001 HIS F 75 PHE 0.020 0.002 PHE X 688 TYR 0.016 0.002 TYR G 39 ARG 0.014 0.001 ARG D 69 Details of bonding type rmsd hydrogen bonds : bond 0.06678 ( 1192) hydrogen bonds : angle 4.25326 ( 3110) covalent geometry : bond 0.00443 (22566) covalent geometry : angle 0.63000 (32133) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9265 (t80) cc_final: 0.8871 (t80) REVERT: A 90 MET cc_start: 0.9383 (mmp) cc_final: 0.9045 (mmm) REVERT: E 67 PHE cc_start: 0.9201 (t80) cc_final: 0.8972 (t80) REVERT: G 102 ILE cc_start: 0.7035 (mp) cc_final: 0.6458 (tt) REVERT: H 59 MET cc_start: 0.9711 (mmm) cc_final: 0.9390 (tmm) REVERT: H 66 ILE cc_start: 0.9344 (pt) cc_final: 0.9134 (pt) REVERT: H 77 LEU cc_start: 0.9787 (tt) cc_final: 0.9548 (pp) REVERT: H 79 HIS cc_start: 0.9475 (m90) cc_final: 0.9103 (m90) REVERT: X 90 MET cc_start: 0.9455 (tmm) cc_final: 0.9220 (tmm) REVERT: X 751 MET cc_start: 0.9284 (ttm) cc_final: 0.8851 (ttm) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.3098 time to fit residues: 31.1586 Evaluate side-chains 49 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 27 optimal weight: 8.9990 chunk 104 optimal weight: 40.0000 chunk 83 optimal weight: 30.0000 chunk 55 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 171 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 chunk 185 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 146 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN H 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 GLN ** X 983 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.031622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.025482 restraints weight = 402258.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.026065 restraints weight = 262336.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.026400 restraints weight = 193384.676| |-----------------------------------------------------------------------------| r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.5726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 22566 Z= 0.272 Angle : 0.688 12.281 32133 Z= 0.390 Chirality : 0.040 0.263 3702 Planarity : 0.005 0.064 2702 Dihedral : 29.992 178.904 6426 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 27.89 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.98 % Favored : 96.95 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: 0.85 (0.21), residues: 1609 helix: 1.35 (0.16), residues: 998 sheet: -1.48 (0.62), residues: 69 loop : -0.55 (0.27), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP X 464 HIS 0.005 0.001 HIS B 75 PHE 0.017 0.002 PHE E 67 TYR 0.018 0.002 TYR G 39 ARG 0.007 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.08708 ( 1192) hydrogen bonds : angle 4.52910 ( 3110) covalent geometry : bond 0.00561 (22566) covalent geometry : angle 0.68843 (32133) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9202 (t80) cc_final: 0.8818 (t80) REVERT: A 78 PHE cc_start: 0.9268 (t80) cc_final: 0.9049 (t80) REVERT: H 56 MET cc_start: 0.8306 (tpt) cc_final: 0.7856 (tpt) REVERT: H 59 MET cc_start: 0.9725 (mmm) cc_final: 0.9352 (tmm) REVERT: H 77 LEU cc_start: 0.9757 (tt) cc_final: 0.9485 (pp) REVERT: H 79 HIS cc_start: 0.9444 (m90) cc_final: 0.9065 (m90) REVERT: X 90 MET cc_start: 0.9434 (tmm) cc_final: 0.9194 (tmm) REVERT: X 383 MET cc_start: 0.8957 (ttm) cc_final: 0.8663 (ttt) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.3196 time to fit residues: 29.5210 Evaluate side-chains 44 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 21 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 164 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 GLN X 983 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.032257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.026035 restraints weight = 395732.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.026633 restraints weight = 254787.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.026989 restraints weight = 187946.485| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22566 Z= 0.209 Angle : 0.640 11.821 32133 Z= 0.363 Chirality : 0.038 0.229 3702 Planarity : 0.004 0.062 2702 Dihedral : 29.790 178.946 6426 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 21.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 1.00 (0.21), residues: 1609 helix: 1.50 (0.16), residues: 993 sheet: -1.27 (0.60), residues: 79 loop : -0.52 (0.27), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X 464 HIS 0.006 0.001 HIS F 75 PHE 0.016 0.002 PHE A 78 TYR 0.018 0.002 TYR H 37 ARG 0.008 0.001 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.06516 ( 1192) hydrogen bonds : angle 4.31944 ( 3110) covalent geometry : bond 0.00436 (22566) covalent geometry : angle 0.63995 (32133) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3218 Ramachandran restraints generated. 1609 Oldfield, 0 Emsley, 1609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 PHE cc_start: 0.9262 (t80) cc_final: 0.8877 (t80) REVERT: E 67 PHE cc_start: 0.9235 (t80) cc_final: 0.9032 (t80) REVERT: H 77 LEU cc_start: 0.9738 (tt) cc_final: 0.9475 (pp) REVERT: H 79 HIS cc_start: 0.9411 (m90) cc_final: 0.9095 (m90) REVERT: X 90 MET cc_start: 0.9400 (tmm) cc_final: 0.9150 (tmm) REVERT: X 751 MET cc_start: 0.9277 (ttm) cc_final: 0.8831 (ttm) REVERT: X 939 MET cc_start: 0.8567 (tmm) cc_final: 0.8345 (tmm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.3375 time to fit residues: 31.2026 Evaluate side-chains 44 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 90 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 68 optimal weight: 0.4980 chunk 109 optimal weight: 0.0870 chunk 47 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 chunk 64 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 overall best weight: 1.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.034200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.027842 restraints weight = 373559.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.028433 restraints weight = 245815.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.028796 restraints weight = 183919.333| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22566 Z= 0.146 Angle : 0.591 9.124 32133 Z= 0.334 Chirality : 0.037 0.212 3702 Planarity : 0.004 0.059 2702 Dihedral : 29.076 177.079 6426 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.42 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % 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: 1.34 (0.21), residues: 1609 helix: 1.79 (0.16), residues: 1000 sheet: -1.21 (0.59), residues: 84 loop : -0.44 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP X1074 HIS 0.006 0.001 HIS A 113 PHE 0.016 0.001 PHE C 25 TYR 0.014 0.001 TYR G 39 ARG 0.006 0.000 ARG E 63 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 1192) hydrogen bonds : angle 3.95541 ( 3110) covalent geometry : bond 0.00309 (22566) covalent geometry : angle 0.59126 (32133) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5286.95 seconds wall clock time: 93 minutes 30.67 seconds (5610.67 seconds total)