Starting phenix.real_space_refine on Sun Mar 17 21:23:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5z_30995/03_2024/7e5z_30995_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5z_30995/03_2024/7e5z_30995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5z_30995/03_2024/7e5z_30995.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5z_30995/03_2024/7e5z_30995.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5z_30995/03_2024/7e5z_30995_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e5z_30995/03_2024/7e5z_30995_updated.pdb" } resolution = 3.6 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= 0.007 sd= 0.034 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: 8 Type Number sf(0) Gaussians W 1 12.54 5 Fe 20 7.16 5 P 5 5.49 5 S 85 5.16 5 C 6389 2.51 5 N 1820 2.21 5 O 1924 1.98 5 H 8810 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 93": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 134": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A ARG 190": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 196": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 289": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 373": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 392": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 397": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A ARG 491": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 502": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 511": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 516": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 584": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 621": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 655": "OE1" <-> "OE2" Residue "A ARG 684": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 692": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A ARG 757": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 772": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 783": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 815": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 818": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 848": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 47": "NH1" <-> "NH2" Residue "B GLU 100": "OE1" <-> "OE2" Residue "B ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 132": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 140": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 172": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B GLU 178": "OE1" <-> "OE2" Residue "B ARG 194": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 236": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 248": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 256": "OE1" <-> "OE2" Residue "B ARG 274": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 303": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 308": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 324": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 363": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 377": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 382": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 392": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 395": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 399": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 500": "OE1" <-> "OE2" Residue "B ARG 509": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 516": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19054 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 11141 Classifications: {'peptide': 775} Link IDs: {'PTRANS': 45, 'TRANS': 729} Chain breaks: 1 Chain: "B" Number of atoms: 7747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 7747 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 27, 'TRANS': 509} Chain: "A" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 123 Unusual residues: {' W': 1, 'FES': 1, 'MGD': 2, 'SF4': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 43 Unusual residues: {'FES': 1, 'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 490 SG CYS A 102 52.690 29.667 81.735 1.00 78.33 S ATOM 676 SG CYS A 115 53.012 27.443 83.224 1.00 81.48 S ATOM 717 SG CYS A 118 57.786 28.789 83.440 1.00 82.89 S ATOM 884 SG CYS A 132 57.079 32.544 81.745 1.00 84.97 S ATOM 2092 SG CYS A 216 45.893 27.696 77.991 1.00 82.89 S ATOM 2057 SG CYS A 213 40.458 26.953 80.445 1.00 83.96 S ATOM 2740 SG CYS A 266 42.889 24.929 74.851 1.00 80.21 S ATOM 2133 SG CYS A 219 42.000 29.786 75.167 1.00 83.24 S ATOM 2191 SG CYS A 223 39.836 35.677 69.737 1.00 81.05 S ATOM 2686 SG CYS A 262 40.099 31.233 69.550 1.00 80.67 S ATOM 2639 SG CYS A 256 35.005 33.064 66.998 1.00 83.00 S ATOM 2657 SG CYS A 259 39.457 35.799 65.522 1.00 78.47 S ATOM 2191 SG CYS A 223 39.836 35.677 69.737 1.00 81.05 S ATOM 2657 SG CYS A 259 39.457 35.799 65.522 1.00 78.47 S ATOM 3176 SG CYS A 295 45.936 34.087 52.188 1.00 86.22 S ATOM 3667 SG CYS A 329 41.258 35.643 56.111 1.00 76.61 S ATOM 3219 SG CYS A 298 41.732 38.713 51.901 1.00 88.24 S ATOM 3176 SG CYS A 295 45.936 34.087 52.188 1.00 86.22 S ATOM 3257 SG CYS A 302 47.040 36.431 55.411 1.00 80.77 S ATOM 18110 SG CYS B 502 45.093 35.317 92.305 1.00 79.77 S ATOM 18610 SG CYS B 542 48.649 35.148 95.664 1.00 83.44 S ATOM 18176 SG CYS B 508 45.577 30.724 93.567 1.00 84.21 S ATOM 18140 SG CYS B 505 48.800 31.120 92.714 1.00 84.95 S ATOM 18610 SG CYS B 542 48.649 35.148 95.664 1.00 83.44 S ATOM 18110 SG CYS B 502 45.093 35.317 92.305 1.00 79.77 S ATOM 18176 SG CYS B 508 45.577 30.724 93.567 1.00 84.21 S ATOM 12410 SG CYS B 113 31.884 36.456 110.142 1.00 78.16 S ATOM 12451 SG CYS B 118 31.038 37.209 113.136 1.00 77.35 S ATOM 12874 SG CYS B 146 35.767 39.161 109.530 1.00 80.98 S ATOM 12924 SG CYS B 150 36.341 38.978 113.213 1.00 78.95 S Time building chain proxies: 8.81, per 1000 atoms: 0.46 Number of scatterers: 19054 At special positions: 0 Unit cell: (88.81, 89.64, 142.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) W 1 73.95 Fe 20 26.01 S 85 16.00 P 5 15.00 O 1924 8.00 N 1820 7.00 C 6389 6.00 H 8810 1.00 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: 14.67 Conformation dependent library (CDL) restraints added in 2.3 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A1003 " pdb="FE2 FES A1003 " - pdb=" SG CYS A 132 " pdb="FE2 FES A1003 " - pdb=" SG CYS A 118 " pdb="FE1 FES A1003 " - pdb=" SG CYS A 102 " pdb="FE1 FES A1003 " - pdb=" SG CYS A 115 " pdb=" FES B1002 " pdb="FE2 FES B1002 " - pdb=" SG CYS B 146 " pdb="FE1 FES B1002 " - pdb=" SG CYS B 113 " pdb="FE2 FES B1002 " - pdb=" SG CYS B 150 " pdb="FE1 FES B1002 " - pdb=" SG CYS B 118 " pdb=" SF4 A1004 " pdb="FE3 SF4 A1004 " - pdb=" SG CYS A 266 " pdb="FE1 SF4 A1004 " - pdb=" SG CYS A 216 " pdb="FE2 SF4 A1004 " - pdb=" SG CYS A 213 " pdb="FE4 SF4 A1004 " - pdb=" SG CYS A 219 " pdb=" SF4 A1005 " pdb="FE4 SF4 A1005 " - pdb=" SG CYS A 259 " pdb="FE4 SF4 A1005 " - pdb=" SG CYS A 223 " pdb="FE2 SF4 A1005 " - pdb=" SG CYS A 256 " pdb="FE1 SF4 A1005 " - pdb=" SG CYS A 262 " pdb=" SF4 A1006 " pdb="FE2 SF4 A1006 " - pdb=" SG CYS A 329 " pdb="FE4 SF4 A1006 " - pdb=" SG CYS A 302 " pdb="FE1 SF4 A1006 " - pdb=" SG CYS A 295 " pdb="FE3 SF4 A1006 " - pdb=" SG CYS A 298 " pdb=" SF4 B1001 " pdb="FE1 SF4 B1001 " - pdb=" SG CYS B 542 " pdb="FE2 SF4 B1001 " - pdb=" SG CYS B 508 " pdb="FE4 SF4 B1001 " - pdb=" SG CYS B 502 " pdb="FE3 SF4 B1001 " - pdb=" SG CYS B 505 " Number of angles added : 62 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2394 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 7 sheets defined 33.1% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.82 Creating SS restraints... Processing helix chain 'A' and resid 87 through 94 Processing helix chain 'A' and resid 148 through 162 Processing helix chain 'A' and resid 176 through 183 Processing helix chain 'A' and resid 218 through 223 Processing helix chain 'A' and resid 246 through 248 No H-bonds generated for 'chain 'A' and resid 246 through 248' Processing helix chain 'A' and resid 330 through 333 No H-bonds generated for 'chain 'A' and resid 330 through 333' Processing helix chain 'A' and resid 379 through 395 removed outlier: 4.058A pdb=" N ALA A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY A 387 " --> pdb=" O ARG A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 423 removed outlier: 3.577A pdb=" N LEU A 415 " --> pdb=" O GLU A 411 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL A 420 " --> pdb=" O PHE A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 473 through 476 No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 478 through 491 Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 520 through 534 removed outlier: 4.085A pdb=" N ILE A 531 " --> pdb=" O MET A 527 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 544 No H-bonds generated for 'chain 'A' and resid 541 through 544' Processing helix chain 'A' and resid 553 through 558 Processing helix chain 'A' and resid 565 through 568 No H-bonds generated for 'chain 'A' and resid 565 through 568' Processing helix chain 'A' and resid 572 through 584 Processing helix chain 'A' and resid 594 through 597 No H-bonds generated for 'chain 'A' and resid 594 through 597' Processing helix chain 'A' and resid 602 through 616 removed outlier: 3.911A pdb=" N CYS A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N ALA A 611 " --> pdb=" O ARG A 607 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU A 612 " --> pdb=" O CYS A 608 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ALA A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU A 614 " --> pdb=" O ILE A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 639 Processing helix chain 'A' and resid 649 through 651 No H-bonds generated for 'chain 'A' and resid 649 through 651' Processing helix chain 'A' and resid 658 through 667 removed outlier: 3.622A pdb=" N LEU A 662 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N PHE A 663 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU A 664 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP A 667 " --> pdb=" O GLU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 686 Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 712 through 716 Processing helix chain 'A' and resid 774 through 785 removed outlier: 3.848A pdb=" N GLN A 779 " --> pdb=" O TRP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 802 removed outlier: 4.637A pdb=" N ALA A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 808 No H-bonds generated for 'chain 'A' and resid 806 through 808' Processing helix chain 'A' and resid 813 through 817 Processing helix chain 'B' and resid 36 through 42 removed outlier: 4.077A pdb=" N LEU B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 62 Processing helix chain 'B' and resid 68 through 78 Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 124 through 130 Processing helix chain 'B' and resid 168 through 176 removed outlier: 4.183A pdb=" N ALA B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 195 Processing helix chain 'B' and resid 200 through 206 removed outlier: 4.129A pdb=" N LEU B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 235 through 243 Processing helix chain 'B' and resid 264 through 268 Processing helix chain 'B' and resid 273 through 286 removed outlier: 3.957A pdb=" N VAL B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 removed outlier: 3.983A pdb=" N ALA B 307 " --> pdb=" O ARG B 303 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ALA B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS B 312 " --> pdb=" O ARG B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 332 Processing helix chain 'B' and resid 334 through 341 Processing helix chain 'B' and resid 370 through 374 Processing helix chain 'B' and resid 376 through 382 removed outlier: 3.571A pdb=" N ARG B 382 " --> pdb=" O ASP B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 387 No H-bonds generated for 'chain 'B' and resid 385 through 387' Processing helix chain 'B' and resid 421 through 426 Processing helix chain 'B' and resid 466 through 468 No H-bonds generated for 'chain 'B' and resid 466 through 468' Processing helix chain 'B' and resid 486 through 499 Processing helix chain 'B' and resid 506 through 518 removed outlier: 4.160A pdb=" N GLN B 513 " --> pdb=" O ARG B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 538 Processing helix chain 'B' and resid 550 through 558 Processing sheet with id= A, first strand: chain 'A' and resid 71 through 74 Processing sheet with id= B, first strand: chain 'A' and resid 206 through 208 removed outlier: 3.566A pdb=" N MET A 272 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 289 through 294 removed outlier: 3.786A pdb=" N ARG A 289 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 308 " --> pdb=" O ARG A 289 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL A 291 " --> pdb=" O TYR A 306 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLU A 317 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR A 315 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LYS A 309 " --> pdb=" O ILE A 313 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 111 through 113 removed outlier: 7.063A pdb=" N VAL B 142 " --> pdb=" O VAL B 112 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 249 through 251 removed outlier: 3.942A pdb=" N LEU B 366 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA B 251 " --> pdb=" O LEU B 366 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 399 through 403 removed outlier: 3.552A pdb=" N VAL B 403 " --> pdb=" O GLY B 411 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY B 411 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 440 through 443 217 hydrogen bonds defined for protein. 624 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.66 Time building geometry restraints manager: 15.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.13: 8800 1.13 - 1.42: 4376 1.42 - 1.71: 5978 1.71 - 2.00: 94 2.00 - 2.29: 56 Bond restraints: 19304 Sorted by residual: bond pdb=" C LEU A 612 " pdb=" O LEU A 612 " ideal model delta sigma weight residual 1.236 1.305 -0.068 1.15e-02 7.56e+03 3.52e+01 bond pdb=" N LEU A 612 " pdb=" CA LEU A 612 " ideal model delta sigma weight residual 1.459 1.513 -0.054 1.19e-02 7.06e+03 2.07e+01 bond pdb=" C10 MGD A1002 " pdb=" O3A MGD A1002 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" N ILE A 615 " pdb=" CA ILE A 615 " ideal model delta sigma weight residual 1.459 1.505 -0.046 1.33e-02 5.65e+03 1.18e+01 bond pdb=" C10 MGD A1001 " pdb=" O3A MGD A1001 " ideal model delta sigma weight residual 1.406 1.471 -0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 19299 not shown) Histogram of bond angle deviations from ideal: 73.53 - 85.62: 48 85.62 - 97.72: 9 97.72 - 109.81: 13674 109.81 - 121.90: 16836 121.90 - 133.99: 3787 Bond angle restraints: 34354 Sorted by residual: angle pdb=" S1 FES A1003 " pdb="FE2 FES A1003 " pdb=" S2 FES A1003 " ideal model delta sigma weight residual 104.33 86.51 17.82 1.14e+00 7.69e-01 2.44e+02 angle pdb=" S1 FES B1002 " pdb="FE2 FES B1002 " pdb=" S2 FES B1002 " ideal model delta sigma weight residual 104.33 87.36 16.97 1.14e+00 7.69e-01 2.21e+02 angle pdb=" S1 FES A1003 " pdb="FE1 FES A1003 " pdb=" S2 FES A1003 " ideal model delta sigma weight residual 104.33 86.48 17.85 1.20e+00 6.94e-01 2.21e+02 angle pdb=" S1 FES B1002 " pdb="FE1 FES B1002 " pdb=" S2 FES B1002 " ideal model delta sigma weight residual 104.33 87.36 16.97 1.20e+00 6.94e-01 2.00e+02 angle pdb="FE1 FES A1003 " pdb=" S2 FES A1003 " pdb="FE2 FES A1003 " ideal model delta sigma weight residual 75.66 85.97 -10.31 1.14e+00 7.69e-01 8.18e+01 ... (remaining 34349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 8990 35.43 - 70.86: 290 70.86 - 106.30: 23 106.30 - 141.73: 0 141.73 - 177.16: 1 Dihedral angle restraints: 9304 sinusoidal: 5051 harmonic: 4253 Sorted by residual: dihedral pdb=" C10 FMN B1000 " pdb=" C1' FMN B1000 " pdb=" N10 FMN B1000 " pdb=" C2' FMN B1000 " ideal model delta sinusoidal sigma weight residual -102.41 74.75 -177.16 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" CA ARG A 237 " pdb=" C ARG A 237 " pdb=" N ALA A 238 " pdb=" CA ALA A 238 " ideal model delta harmonic sigma weight residual -180.00 -156.81 -23.19 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" C ALA B 153 " pdb=" N ALA B 153 " pdb=" CA ALA B 153 " pdb=" CB ALA B 153 " ideal model delta harmonic sigma weight residual -122.60 -134.15 11.55 0 2.50e+00 1.60e-01 2.13e+01 ... (remaining 9301 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1412 0.077 - 0.154: 146 0.154 - 0.232: 6 0.232 - 0.309: 3 0.309 - 0.386: 2 Chirality restraints: 1569 Sorted by residual: chirality pdb=" CA ALA B 153 " pdb=" N ALA B 153 " pdb=" C ALA B 153 " pdb=" CB ALA B 153 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.39 2.00e-01 2.50e+01 3.72e+00 chirality pdb=" C11 MGD A1001 " pdb=" C10 MGD A1001 " pdb=" C12 MGD A1001 " pdb=" O11 MGD A1001 " both_signs ideal model delta sigma weight residual False 2.43 2.11 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" C23 MGD A1002 " pdb=" C14 MGD A1002 " pdb=" N22 MGD A1002 " pdb=" O11 MGD A1002 " both_signs ideal model delta sigma weight residual False 2.33 2.59 -0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 1566 not shown) Planarity restraints: 3008 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 MGD A1002 " -0.078 2.00e-02 2.50e+03 1.70e-01 7.96e+02 pdb=" C17 MGD A1002 " 0.016 2.00e-02 2.50e+03 pdb=" C19 MGD A1002 " 0.025 2.00e-02 2.50e+03 pdb=" C21 MGD A1002 " -0.152 2.00e-02 2.50e+03 pdb=" C23 MGD A1002 " 0.438 2.00e-02 2.50e+03 pdb=" N15 MGD A1002 " -0.173 2.00e-02 2.50e+03 pdb=" N18 MGD A1002 " 0.071 2.00e-02 2.50e+03 pdb=" N19 MGD A1002 " 0.087 2.00e-02 2.50e+03 pdb=" N20 MGD A1002 " -0.079 2.00e-02 2.50e+03 pdb=" N22 MGD A1002 " -0.212 2.00e-02 2.50e+03 pdb=" O17 MGD A1002 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 MGD A1001 " 0.062 2.00e-02 2.50e+03 1.42e-01 5.55e+02 pdb=" C17 MGD A1001 " -0.014 2.00e-02 2.50e+03 pdb=" C19 MGD A1001 " -0.020 2.00e-02 2.50e+03 pdb=" C21 MGD A1001 " 0.121 2.00e-02 2.50e+03 pdb=" C23 MGD A1001 " -0.363 2.00e-02 2.50e+03 pdb=" N15 MGD A1001 " 0.139 2.00e-02 2.50e+03 pdb=" N18 MGD A1001 " -0.059 2.00e-02 2.50e+03 pdb=" N19 MGD A1001 " -0.074 2.00e-02 2.50e+03 pdb=" N20 MGD A1001 " 0.064 2.00e-02 2.50e+03 pdb=" N22 MGD A1001 " 0.191 2.00e-02 2.50e+03 pdb=" O17 MGD A1001 " -0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 529 " 0.071 2.00e-02 2.50e+03 7.53e-02 8.51e+01 pdb=" CG ASN A 529 " -0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 529 " -0.068 2.00e-02 2.50e+03 pdb=" ND2 ASN A 529 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 529 " -0.109 2.00e-02 2.50e+03 pdb="HD22 ASN A 529 " 0.111 2.00e-02 2.50e+03 ... (remaining 3005 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.05: 308 2.05 - 2.69: 28546 2.69 - 3.33: 51284 3.33 - 3.96: 63376 3.96 - 4.60: 100069 Nonbonded interactions: 243583 Sorted by model distance: nonbonded pdb="HD13 LEU A 536 " pdb="HH22 ARG A 584 " model vdw 1.419 2.270 nonbonded pdb=" O PHE A 751 " pdb=" H GLN A 759 " model vdw 1.499 1.850 nonbonded pdb=" OG1 THR A 454 " pdb=" H LEU A 626 " model vdw 1.579 1.850 nonbonded pdb=" HB3 PHE A 457 " pdb=" HE1 HIS A 627 " model vdw 1.599 2.270 nonbonded pdb=" H GLN A 82 " pdb=" OE1 GLU A 85 " model vdw 1.621 1.850 ... (remaining 243578 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: 0.600 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: 0.290 Extract box with map and model: 3.860 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 64.070 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 0.078 10494 Z= 0.332 Angle : 0.911 20.615 14303 Z= 0.540 Chirality : 0.048 0.386 1569 Planarity : 0.007 0.170 1865 Dihedral : 15.297 177.162 3907 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 21.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.18 % Favored : 89.74 % Rotamer: Outliers : 0.57 % Allowed : 3.33 % Favored : 96.10 % Cbeta Deviations : 0.08 % 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: -6.25 (0.16), residues: 1306 helix: -3.41 (0.18), residues: 446 sheet: -4.61 (0.35), residues: 95 loop : -4.82 (0.15), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 524 HIS 0.008 0.001 HIS B 33 PHE 0.009 0.001 PHE A 744 TYR 0.009 0.001 TYR A 582 ARG 0.008 0.001 ARG A 815 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 188 time to evaluate : 1.717 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.8120 (tpp) cc_final: 0.7901 (tpt) REVERT: A 472 ASN cc_start: 0.7922 (t0) cc_final: 0.7626 (t0) REVERT: A 545 TYR cc_start: 0.7907 (m-80) cc_final: 0.7474 (m-10) REVERT: B 129 THR cc_start: 0.7611 (m) cc_final: 0.7261 (m) REVERT: B 256 GLU cc_start: 0.7253 (pt0) cc_final: 0.6431 (pt0) REVERT: B 264 ASP cc_start: 0.7306 (m-30) cc_final: 0.7098 (m-30) outliers start: 6 outliers final: 4 residues processed: 192 average time/residue: 0.5043 time to fit residues: 132.7003 Evaluate side-chains 127 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 123 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 852 VAL Chi-restraints excluded: chain B residue 154 PRO Chi-restraints excluded: chain B residue 366 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 101 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 118 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 486 ASN A 490 GLN A 508 HIS A 540 GLN ** A 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 636 GLN A 669 GLN A 724 GLN A 779 GLN A 831 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10494 Z= 0.229 Angle : 0.587 8.550 14303 Z= 0.296 Chirality : 0.043 0.188 1569 Planarity : 0.004 0.041 1865 Dihedral : 11.038 174.828 1575 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.64 % Favored : 89.28 % Rotamer: Outliers : 1.05 % Allowed : 8.94 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.19), residues: 1306 helix: -2.20 (0.22), residues: 455 sheet: -3.86 (0.41), residues: 98 loop : -4.08 (0.18), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 524 HIS 0.006 0.001 HIS A 627 PHE 0.017 0.001 PHE A 744 TYR 0.012 0.001 TYR A 414 ARG 0.006 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 128 time to evaluate : 1.437 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 ASP cc_start: 0.7801 (t0) cc_final: 0.7369 (t70) REVERT: A 594 MET cc_start: 0.6837 (mmp) cc_final: 0.6467 (mmt) REVERT: B 54 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7278 (mm-30) REVERT: B 176 GLU cc_start: 0.7754 (tp30) cc_final: 0.7464 (tp30) REVERT: B 256 GLU cc_start: 0.7851 (pt0) cc_final: 0.7138 (pt0) REVERT: B 264 ASP cc_start: 0.7411 (m-30) cc_final: 0.7186 (m-30) outliers start: 11 outliers final: 8 residues processed: 136 average time/residue: 0.4075 time to fit residues: 81.1586 Evaluate side-chains 122 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 223 CYS Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 568 CYS Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 561 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 98 optimal weight: 0.0770 chunk 80 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 118 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 overall best weight: 2.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 10494 Z= 0.291 Angle : 0.587 6.614 14303 Z= 0.301 Chirality : 0.044 0.154 1569 Planarity : 0.004 0.044 1865 Dihedral : 10.637 174.281 1571 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.57 % Favored : 89.36 % Rotamer: Outliers : 1.71 % Allowed : 11.42 % Favored : 86.87 % 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: -4.19 (0.21), residues: 1306 helix: -1.67 (0.23), residues: 471 sheet: -3.19 (0.48), residues: 96 loop : -3.66 (0.19), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 524 HIS 0.005 0.001 HIS B 390 PHE 0.020 0.001 PHE A 744 TYR 0.011 0.001 TYR A 315 ARG 0.003 0.000 ARG A 818 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 141 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 1.256 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: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7479 (mtp180) REVERT: A 112 ASP cc_start: 0.8029 (t0) cc_final: 0.7713 (t70) REVERT: A 131 SER cc_start: 0.9324 (t) cc_final: 0.8837 (p) REVERT: A 594 MET cc_start: 0.6953 (mmp) cc_final: 0.6496 (mmt) REVERT: B 54 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7548 (mm-30) REVERT: B 351 LYS cc_start: 0.8778 (mmmm) cc_final: 0.8510 (tppt) REVERT: B 549 SER cc_start: 0.9125 (m) cc_final: 0.8751 (p) outliers start: 18 outliers final: 12 residues processed: 134 average time/residue: 0.4045 time to fit residues: 79.5226 Evaluate side-chains 122 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 791 TYR Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 561 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 13 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 118 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 112 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 10494 Z= 0.151 Angle : 0.504 6.595 14303 Z= 0.256 Chirality : 0.040 0.136 1569 Planarity : 0.003 0.048 1865 Dihedral : 8.987 176.093 1570 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.89 % Favored : 92.04 % Rotamer: Outliers : 1.05 % Allowed : 13.23 % Favored : 85.73 % 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: -3.49 (0.22), residues: 1306 helix: -1.08 (0.25), residues: 471 sheet: -3.03 (0.46), residues: 103 loop : -3.20 (0.21), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 592 HIS 0.002 0.001 HIS B 390 PHE 0.015 0.001 PHE A 744 TYR 0.011 0.001 TYR A 315 ARG 0.002 0.000 ARG A 507 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 122 time to evaluate : 1.571 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 112 ASP cc_start: 0.7952 (t0) cc_final: 0.7614 (t70) REVERT: A 131 SER cc_start: 0.9284 (t) cc_final: 0.8863 (p) REVERT: A 251 MET cc_start: 0.8326 (tmm) cc_final: 0.8113 (tmm) REVERT: A 523 MET cc_start: 0.7541 (ptm) cc_final: 0.7144 (ptm) REVERT: A 594 MET cc_start: 0.6770 (mmp) cc_final: 0.6272 (mmt) REVERT: B 54 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7472 (mm-30) REVERT: B 256 GLU cc_start: 0.7949 (pt0) cc_final: 0.7730 (pt0) REVERT: B 351 LYS cc_start: 0.8707 (mmmm) cc_final: 0.8459 (tppt) outliers start: 11 outliers final: 7 residues processed: 129 average time/residue: 0.4015 time to fit residues: 76.6546 Evaluate side-chains 116 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 109 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 501 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 93 optimal weight: 0.0270 chunk 51 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 112 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10494 Z= 0.253 Angle : 0.541 5.237 14303 Z= 0.279 Chirality : 0.042 0.142 1569 Planarity : 0.004 0.052 1865 Dihedral : 9.239 175.176 1568 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.57 % Favored : 89.36 % Rotamer: Outliers : 1.52 % Allowed : 13.51 % Favored : 84.97 % 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: -3.32 (0.23), residues: 1306 helix: -0.89 (0.25), residues: 470 sheet: -3.29 (0.46), residues: 101 loop : -3.07 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 524 HIS 0.004 0.001 HIS B 390 PHE 0.016 0.001 PHE A 744 TYR 0.010 0.001 TYR A 315 ARG 0.002 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 116 time to evaluate : 1.567 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 112 ASP cc_start: 0.8146 (t0) cc_final: 0.7895 (t70) REVERT: A 131 SER cc_start: 0.9363 (t) cc_final: 0.8905 (p) REVERT: A 523 MET cc_start: 0.7669 (ptm) cc_final: 0.7317 (ptm) REVERT: A 594 MET cc_start: 0.6939 (mmp) cc_final: 0.6318 (mmt) REVERT: B 54 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7651 (mm-30) REVERT: B 351 LYS cc_start: 0.8723 (mmmm) cc_final: 0.8477 (tppt) REVERT: B 549 SER cc_start: 0.9149 (m) cc_final: 0.8812 (p) outliers start: 16 outliers final: 13 residues processed: 125 average time/residue: 0.3926 time to fit residues: 73.6210 Evaluate side-chains 122 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 109 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 791 TYR Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 561 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 125 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 449 ASN ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10494 Z= 0.279 Angle : 0.554 5.222 14303 Z= 0.286 Chirality : 0.043 0.144 1569 Planarity : 0.004 0.050 1865 Dihedral : 9.328 177.301 1568 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.95 % Favored : 88.97 % Rotamer: Outliers : 2.19 % Allowed : 14.37 % Favored : 83.44 % 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: -3.17 (0.23), residues: 1306 helix: -0.72 (0.25), residues: 460 sheet: -3.23 (0.46), residues: 101 loop : -2.99 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 524 HIS 0.004 0.001 HIS B 390 PHE 0.015 0.001 PHE A 744 TYR 0.010 0.001 TYR A 824 ARG 0.002 0.000 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 110 time to evaluate : 1.444 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 112 ASP cc_start: 0.8249 (t0) cc_final: 0.7988 (t70) REVERT: A 114 ASN cc_start: 0.8935 (OUTLIER) cc_final: 0.8710 (m-40) REVERT: A 131 SER cc_start: 0.9399 (t) cc_final: 0.8949 (p) REVERT: A 594 MET cc_start: 0.6742 (mmp) cc_final: 0.6182 (mmt) REVERT: B 54 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7695 (mm-30) outliers start: 23 outliers final: 18 residues processed: 125 average time/residue: 0.3832 time to fit residues: 71.7656 Evaluate side-chains 123 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 1.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASN Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 598 GLN Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 791 TYR Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 561 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10494 Z= 0.265 Angle : 0.548 5.296 14303 Z= 0.283 Chirality : 0.042 0.141 1569 Planarity : 0.004 0.052 1865 Dihedral : 9.201 176.898 1568 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.95 % Favored : 88.97 % Rotamer: Outliers : 1.81 % Allowed : 15.89 % Favored : 82.30 % 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: -3.01 (0.23), residues: 1306 helix: -0.63 (0.25), residues: 461 sheet: -2.94 (0.47), residues: 105 loop : -2.89 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 524 HIS 0.004 0.001 HIS B 390 PHE 0.015 0.001 PHE A 744 TYR 0.011 0.001 TYR A 824 ARG 0.003 0.000 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 107 time to evaluate : 1.611 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 102 CYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7950 (p) REVERT: A 131 SER cc_start: 0.9391 (t) cc_final: 0.8965 (p) REVERT: A 523 MET cc_start: 0.7668 (ptm) cc_final: 0.7464 (ptm) REVERT: A 594 MET cc_start: 0.6753 (mmp) cc_final: 0.6179 (mmt) REVERT: B 549 SER cc_start: 0.9166 (m) cc_final: 0.8838 (p) outliers start: 19 outliers final: 17 residues processed: 118 average time/residue: 0.3970 time to fit residues: 70.0439 Evaluate side-chains 122 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 104 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 791 TYR Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 561 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 10494 Z= 0.336 Angle : 0.598 8.970 14303 Z= 0.309 Chirality : 0.044 0.146 1569 Planarity : 0.004 0.058 1865 Dihedral : 9.532 176.320 1568 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.02 % Favored : 87.90 % Rotamer: Outliers : 2.38 % Allowed : 16.37 % Favored : 81.26 % 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: -3.11 (0.22), residues: 1306 helix: -0.78 (0.24), residues: 471 sheet: -2.85 (0.49), residues: 94 loop : -2.96 (0.21), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 524 HIS 0.005 0.001 HIS B 390 PHE 0.014 0.001 PHE A 744 TYR 0.012 0.001 TYR A 824 ARG 0.009 0.000 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 133 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 108 time to evaluate : 1.530 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: symmetry clash REVERT: A 102 CYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7856 (p) REVERT: A 131 SER cc_start: 0.9427 (t) cc_final: 0.8987 (p) REVERT: A 594 MET cc_start: 0.6811 (mmp) cc_final: 0.6194 (mmt) REVERT: A 739 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6904 (mt) REVERT: B 549 SER cc_start: 0.9149 (m) cc_final: 0.8910 (p) outliers start: 25 outliers final: 18 residues processed: 125 average time/residue: 0.3945 time to fit residues: 74.2303 Evaluate side-chains 125 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 PHE Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain A residue 734 HIS Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 791 TYR Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 157 GLU Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 561 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10494 Z= 0.174 Angle : 0.522 5.777 14303 Z= 0.267 Chirality : 0.041 0.147 1569 Planarity : 0.004 0.054 1865 Dihedral : 8.867 178.164 1568 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.26 % Favored : 90.66 % Rotamer: Outliers : 1.71 % Allowed : 17.32 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.23), residues: 1306 helix: -0.43 (0.25), residues: 462 sheet: -2.61 (0.52), residues: 92 loop : -2.70 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 524 HIS 0.002 0.001 HIS B 284 PHE 0.014 0.001 PHE A 744 TYR 0.010 0.001 TYR A 315 ARG 0.009 0.000 ARG A 584 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.664 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 102 CYS cc_start: 0.8454 (OUTLIER) cc_final: 0.7898 (p) REVERT: A 131 SER cc_start: 0.9384 (t) cc_final: 0.8993 (p) REVERT: A 135 THR cc_start: 0.9306 (t) cc_final: 0.8898 (m) REVERT: A 594 MET cc_start: 0.6828 (mmp) cc_final: 0.6190 (mmt) REVERT: B 549 SER cc_start: 0.9152 (m) cc_final: 0.8853 (p) outliers start: 18 outliers final: 12 residues processed: 121 average time/residue: 0.4083 time to fit residues: 73.3426 Evaluate side-chains 120 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 561 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10494 Z= 0.216 Angle : 0.538 8.462 14303 Z= 0.274 Chirality : 0.041 0.143 1569 Planarity : 0.004 0.053 1865 Dihedral : 8.890 177.790 1568 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.18 % Favored : 89.74 % Rotamer: Outliers : 1.33 % Allowed : 17.41 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.23), residues: 1306 helix: -0.30 (0.25), residues: 460 sheet: -2.53 (0.53), residues: 87 loop : -2.63 (0.22), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 524 HIS 0.003 0.001 HIS B 390 PHE 0.017 0.001 PHE B 361 TYR 0.011 0.001 TYR A 824 ARG 0.012 0.000 ARG A 584 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue VAL 127 is missing expected H atoms. Skipping. Residue LEU 128 is missing expected H atoms. Skipping. Residue VAL 142 is missing expected H atoms. Skipping. Residue VAL 183 is missing expected H atoms. Skipping. Residue LEU 184 is missing expected H atoms. Skipping. Residue THR 187 is missing expected H atoms. Skipping. Residue SER 189 is missing expected H atoms. Skipping. Residue ILE 214 is missing expected H atoms. Skipping. Residue SER 405 is missing expected H atoms. Skipping. Residue LYS 485 is missing expected H atoms. Skipping. Residue MET 594 is missing expected H atoms. Skipping. Residue ILE 691 is missing expected H atoms. Skipping. Residue ALA 34 is missing expected H atoms. Skipping. Residue THR 117 is missing expected H atoms. Skipping. Residue THR 180 is missing expected H atoms. Skipping. Residue THR 270 is missing expected H atoms. Skipping. Residue LEU 313 is missing expected H atoms. Skipping. Residue ILE 330 is missing expected H atoms. Skipping. Residue SER 400 is missing expected H atoms. Skipping. Residue MET 455 is missing expected H atoms. Skipping. Residue TYR 468 is missing expected H atoms. Skipping. Residue LEU 518 is missing expected H atoms. Skipping. Residue MET 519 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.529 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 102 CYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7925 (p) REVERT: A 131 SER cc_start: 0.9388 (t) cc_final: 0.9003 (p) REVERT: A 135 THR cc_start: 0.9311 (t) cc_final: 0.8902 (m) REVERT: A 594 MET cc_start: 0.6904 (mmp) cc_final: 0.6242 (mmt) REVERT: B 549 SER cc_start: 0.9161 (m) cc_final: 0.8866 (p) outliers start: 14 outliers final: 12 residues processed: 120 average time/residue: 0.4053 time to fit residues: 72.3010 Evaluate side-chains 124 residues out of total 1051 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 CYS Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain A residue 334 PHE Chi-restraints excluded: chain A residue 410 ASN Chi-restraints excluded: chain B residue 33 HIS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 366 LEU Chi-restraints excluded: chain B residue 501 SER Chi-restraints excluded: chain B residue 561 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 5.9990 chunk 95 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.089693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.080735 restraints weight = 60864.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.083253 restraints weight = 24286.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.084769 restraints weight = 12038.305| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10494 Z= 0.208 Angle : 0.530 8.069 14303 Z= 0.270 Chirality : 0.041 0.142 1569 Planarity : 0.004 0.053 1865 Dihedral : 8.796 178.122 1568 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.95 % Favored : 89.97 % Rotamer: Outliers : 1.43 % Allowed : 17.32 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.23), residues: 1306 helix: -0.25 (0.26), residues: 462 sheet: -2.41 (0.58), residues: 75 loop : -2.58 (0.22), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 524 HIS 0.003 0.001 HIS A 720 PHE 0.020 0.001 PHE A 744 TYR 0.010 0.001 TYR A 824 ARG 0.005 0.000 ARG A 584 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3611.55 seconds wall clock time: 65 minutes 19.11 seconds (3919.11 seconds total)