Starting phenix.real_space_refine on Sun Mar 17 19:56:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2u_23141/03_2024/7l2u_23141_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2u_23141/03_2024/7l2u_23141.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2u_23141/03_2024/7l2u_23141_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2u_23141/03_2024/7l2u_23141_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2u_23141/03_2024/7l2u_23141_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2u_23141/03_2024/7l2u_23141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2u_23141/03_2024/7l2u_23141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2u_23141/03_2024/7l2u_23141_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7l2u_23141/03_2024/7l2u_23141_updated.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 126 5.16 5 Na 2 4.78 5 C 12300 2.51 5 N 2987 2.21 5 O 3394 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18817 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4322 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 518} Chain breaks: 1 Chain: "F" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 591 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "E" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 590 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "B" Number of atoms: 4329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4329 Classifications: {'peptide': 533} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 518} Chain breaks: 1 Chain: "C" Number of atoms: 4367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4367 Classifications: {'peptide': 538} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 523} Chain breaks: 1 Chain: "D" Number of atoms: 4314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4314 Classifications: {'peptide': 532} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 517} Chain breaks: 1 Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {' NA': 1, 'XJ7': 1, 'XKP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'XKP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'XKP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {' NA': 1, 'XJ7': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'XJ7': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 9.75, per 1000 atoms: 0.52 Number of scatterers: 18817 At special positions: 0 Unit cell: (129.018, 129.866, 123.076, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 126 16.00 P 8 15.00 Na 2 11.00 O 3394 8.00 N 2987 7.00 C 12300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS F 2 " - pdb=" SG CYS F 16 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 23 " distance=2.04 Simple disulfide: pdb=" SG CYS F 15 " - pdb=" SG CYS F 31 " distance=2.03 Simple disulfide: pdb=" SG CYS F 44 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 51 " - pdb=" SG CYS F 63 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 71 " distance=2.03 Simple disulfide: pdb=" SG CYS E 2 " - pdb=" SG CYS E 16 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 23 " distance=2.04 Simple disulfide: pdb=" SG CYS E 15 " - pdb=" SG CYS E 31 " distance=2.03 Simple disulfide: pdb=" SG CYS E 44 " - pdb=" SG CYS E 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 51 " - pdb=" SG CYS E 63 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 71 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.41 Conformation dependent library (CDL) restraints added in 3.0 seconds 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4324 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 97 helices and 6 sheets defined 53.5% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.47 Creating SS restraints... Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 214 through 222 Processing helix chain 'A' and resid 234 through 236 No H-bonds generated for 'chain 'A' and resid 234 through 236' Processing helix chain 'A' and resid 251 through 257 Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 287 through 293 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 346 through 354 removed outlier: 3.699A pdb=" N GLN A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 428 removed outlier: 3.784A pdb=" N ARG A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 505 through 507 No H-bonds generated for 'chain 'A' and resid 505 through 507' Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 537 through 556 removed outlier: 3.786A pdb=" N PHE A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU A 553 " --> pdb=" O TRP A 549 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N TYR A 554 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N TYR A 555 " --> pdb=" O ASN A 551 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR A 556 " --> pdb=" O MET A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 575 removed outlier: 3.894A pdb=" N ILE A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR A 565 " --> pdb=" O GLN A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 598 removed outlier: 3.594A pdb=" N PHE A 582 " --> pdb=" O CYS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 642 removed outlier: 3.925A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 642 " --> pdb=" O PHE A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 683 removed outlier: 3.990A pdb=" N GLY A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 711 removed outlier: 4.617A pdb=" N LYS A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N TRP A 697 " --> pdb=" O SER A 693 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 261 through 269 Processing helix chain 'B' and resid 287 through 293 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 346 through 354 removed outlier: 4.219A pdb=" N GLN B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 428 removed outlier: 3.735A pdb=" N ARG B 420 " --> pdb=" O GLU B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 497 removed outlier: 3.834A pdb=" N GLY B 484 " --> pdb=" O LEU B 480 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY B 485 " --> pdb=" O SER B 481 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE B 496 " --> pdb=" O GLY B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 505 through 507 No H-bonds generated for 'chain 'B' and resid 505 through 507' Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 535 through 556 removed outlier: 3.583A pdb=" N VAL B 538 " --> pdb=" O LYS B 535 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N MET B 547 " --> pdb=" O SER B 544 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TRP B 549 " --> pdb=" O ALA B 546 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASN B 551 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 598 removed outlier: 4.140A pdb=" N TYR B 565 " --> pdb=" O GLN B 561 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N CYS B 578 " --> pdb=" O LEU B 574 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG B 579 " --> pdb=" O ARG B 575 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 598 " --> pdb=" O ALA B 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 642 removed outlier: 4.101A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE B 642 " --> pdb=" O PHE B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 682 removed outlier: 3.511A pdb=" N MET B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 710 removed outlier: 4.046A pdb=" N LYS B 694 " --> pdb=" O ALA B 690 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN B 695 " --> pdb=" O GLN B 691 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 210 Processing helix chain 'C' and resid 214 through 222 Processing helix chain 'C' and resid 251 through 257 Processing helix chain 'C' and resid 261 through 269 Processing helix chain 'C' and resid 287 through 293 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 353 removed outlier: 3.693A pdb=" N TYR C 351 " --> pdb=" O GLY C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 412 through 414 No H-bonds generated for 'chain 'C' and resid 412 through 414' Processing helix chain 'C' and resid 416 through 428 removed outlier: 4.113A pdb=" N ARG C 420 " --> pdb=" O GLU C 416 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLN C 423 " --> pdb=" O ASN C 419 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 499 removed outlier: 3.769A pdb=" N GLN C 498 " --> pdb=" O GLN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 503 through 508 Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 535 through 556 removed outlier: 4.041A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N MET C 547 " --> pdb=" O SER C 544 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP C 549 " --> pdb=" O ALA C 546 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN C 551 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 575 removed outlier: 3.857A pdb=" N ILE C 564 " --> pdb=" O GLN C 560 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR C 565 " --> pdb=" O GLN C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 598 removed outlier: 3.799A pdb=" N PHE C 582 " --> pdb=" O CYS C 578 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 642 removed outlier: 4.005A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE C 642 " --> pdb=" O PHE C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 659 through 684 removed outlier: 3.790A pdb=" N GLU C 684 " --> pdb=" O ALA C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 692 No H-bonds generated for 'chain 'C' and resid 689 through 692' Processing helix chain 'C' and resid 696 through 711 Processing helix chain 'D' and resid 204 through 210 Processing helix chain 'D' and resid 215 through 222 Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 251 through 257 Processing helix chain 'D' and resid 261 through 269 Processing helix chain 'D' and resid 287 through 293 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 354 removed outlier: 3.637A pdb=" N TYR D 351 " --> pdb=" O GLY D 347 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLN D 354 " --> pdb=" O ALA D 350 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 412 through 414 No H-bonds generated for 'chain 'D' and resid 412 through 414' Processing helix chain 'D' and resid 416 through 428 removed outlier: 3.826A pdb=" N ARG D 420 " --> pdb=" O GLU D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 503 through 506 No H-bonds generated for 'chain 'D' and resid 503 through 506' Processing helix chain 'D' and resid 511 through 531 removed outlier: 3.532A pdb=" N LEU D 515 " --> pdb=" O TYR D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 556 Processing helix chain 'D' and resid 560 through 575 removed outlier: 4.398A pdb=" N ILE D 564 " --> pdb=" O GLN D 560 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TYR D 565 " --> pdb=" O GLN D 561 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU D 574 " --> pdb=" O GLU D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 598 Processing helix chain 'D' and resid 630 through 641 removed outlier: 4.099A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 659 through 684 removed outlier: 3.914A pdb=" N GLY D 683 " --> pdb=" O ILE D 679 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU D 684 " --> pdb=" O ALA D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 689 through 692 No H-bonds generated for 'chain 'D' and resid 689 through 692' Processing helix chain 'D' and resid 695 through 710 Processing sheet with id= A, first strand: chain 'A' and resid 741 through 747 removed outlier: 3.541A pdb=" N TRP A 372 " --> pdb=" O SER A 379 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ASP A 383 " --> pdb=" O LYS A 368 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYS A 368 " --> pdb=" O ASP A 383 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 21 through 23 Processing sheet with id= C, first strand: chain 'E' and resid 61 through 63 Processing sheet with id= D, first strand: chain 'B' and resid 741 through 747 removed outlier: 3.648A pdb=" N TRP B 372 " --> pdb=" O SER B 379 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ASP B 383 " --> pdb=" O LYS B 368 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS B 368 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 741 through 747 removed outlier: 3.555A pdb=" N TRP C 372 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ASP C 383 " --> pdb=" O LYS C 368 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS C 368 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 741 through 747 removed outlier: 3.578A pdb=" N TRP D 372 " --> pdb=" O SER D 379 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ASP D 383 " --> pdb=" O LYS D 368 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS D 368 " --> pdb=" O ASP D 383 " (cutoff:3.500A) 823 hydrogen bonds defined for protein. 2328 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: 5.33 Time building geometry restraints manager: 7.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2910 1.31 - 1.44: 5480 1.44 - 1.56: 10654 1.56 - 1.69: 16 1.69 - 1.82: 192 Bond restraints: 19252 Sorted by residual: bond pdb=" C11 XKP F 902 " pdb=" O6 XKP F 902 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C5 XKP F 901 " pdb=" O1 XKP F 901 " ideal model delta sigma weight residual 1.338 1.405 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C11 XKP A 802 " pdb=" O6 XKP A 802 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.00e-02 2.50e+03 1.06e+01 bond pdb=" C11 XKP E 901 " pdb=" O6 XKP E 901 " ideal model delta sigma weight residual 1.334 1.399 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C5 XKP E 901 " pdb=" O1 XKP E 901 " ideal model delta sigma weight residual 1.338 1.402 -0.064 2.00e-02 2.50e+03 1.02e+01 ... (remaining 19247 not shown) Histogram of bond angle deviations from ideal: 99.75 - 106.60: 409 106.60 - 113.45: 10288 113.45 - 120.30: 7541 120.30 - 127.14: 7616 127.14 - 133.99: 173 Bond angle restraints: 26027 Sorted by residual: angle pdb=" C SER C 711 " pdb=" N PHE C 712 " pdb=" CA PHE C 712 " ideal model delta sigma weight residual 121.54 130.86 -9.32 1.91e+00 2.74e-01 2.38e+01 angle pdb=" O2 XKP F 901 " pdb=" P XKP F 901 " pdb=" O5 XKP F 901 " ideal model delta sigma weight residual 97.10 111.07 -13.97 3.00e+00 1.11e-01 2.17e+01 angle pdb=" O2 XKP F 902 " pdb=" P XKP F 902 " pdb=" O5 XKP F 902 " ideal model delta sigma weight residual 97.10 110.69 -13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C SER A 711 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta sigma weight residual 121.54 129.80 -8.26 1.91e+00 2.74e-01 1.87e+01 angle pdb=" O3 XKP F 901 " pdb=" P XKP F 901 " pdb=" O4 XKP F 901 " ideal model delta sigma weight residual 121.27 108.72 12.55 3.00e+00 1.11e-01 1.75e+01 ... (remaining 26022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 11277 35.59 - 71.18: 131 71.18 - 106.77: 27 106.77 - 142.36: 4 142.36 - 177.95: 7 Dihedral angle restraints: 11446 sinusoidal: 4712 harmonic: 6734 Sorted by residual: dihedral pdb=" CA ALA C 657 " pdb=" C ALA C 657 " pdb=" N VAL C 658 " pdb=" CA VAL C 658 " ideal model delta harmonic sigma weight residual 180.00 154.65 25.35 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA ALA A 657 " pdb=" C ALA A 657 " pdb=" N VAL A 658 " pdb=" CA VAL A 658 " ideal model delta harmonic sigma weight residual 180.00 155.80 24.20 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" C6 XKP F 902 " pdb=" C7 XKP F 902 " pdb=" C8 XKP F 902 " pdb=" O2 XKP F 902 " ideal model delta sinusoidal sigma weight residual -67.90 110.05 -177.95 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 11443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 2893 1.007 - 2.014: 0 2.014 - 3.021: 0 3.021 - 4.029: 0 4.029 - 5.036: 8 Chirality restraints: 2901 Sorted by residual: chirality pdb=" C3 XJ7 B 801 " pdb=" C2 XJ7 B 801 " pdb=" C24 XJ7 B 801 " pdb=" O3 XJ7 B 801 " both_signs ideal model delta sigma weight residual False -2.50 2.53 -5.04 2.00e-01 2.50e+01 6.34e+02 chirality pdb=" C3 XJ7 D 801 " pdb=" C2 XJ7 D 801 " pdb=" C24 XJ7 D 801 " pdb=" O3 XJ7 D 801 " both_signs ideal model delta sigma weight residual False -2.50 2.53 -5.03 2.00e-01 2.50e+01 6.32e+02 chirality pdb=" C3 XJ7 A 801 " pdb=" C2 XJ7 A 801 " pdb=" C24 XJ7 A 801 " pdb=" O3 XJ7 A 801 " both_signs ideal model delta sigma weight residual False -2.50 2.52 -5.02 2.00e-01 2.50e+01 6.31e+02 ... (remaining 2898 not shown) Planarity restraints: 3205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS D 694 " -0.019 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C LYS D 694 " 0.064 2.00e-02 2.50e+03 pdb=" O LYS D 694 " -0.024 2.00e-02 2.50e+03 pdb=" N ASN D 695 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 711 " -0.009 2.00e-02 2.50e+03 1.88e-02 3.52e+00 pdb=" C SER C 711 " 0.032 2.00e-02 2.50e+03 pdb=" O SER C 711 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE C 712 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 544 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C SER A 544 " -0.028 2.00e-02 2.50e+03 pdb=" O SER A 544 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 545 " 0.009 2.00e-02 2.50e+03 ... (remaining 3202 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 337 2.70 - 3.25: 18762 3.25 - 3.80: 28065 3.80 - 4.35: 36208 4.35 - 4.90: 61341 Nonbonded interactions: 144713 Sorted by model distance: nonbonded pdb=" OG1 THR A 731 " pdb=" OD1 ASP A 733 " model vdw 2.155 2.440 nonbonded pdb=" OG1 THR B 731 " pdb=" OD1 ASP B 733 " model vdw 2.218 2.440 nonbonded pdb=" OD2 ASP A 733 " pdb=" NZ LYS A 735 " model vdw 2.258 2.520 nonbonded pdb=" NZ LYS C 425 " pdb=" OE1 GLU C 709 " model vdw 2.284 2.520 nonbonded pdb=" OD1 ASP B 281 " pdb=" N ASN B 285 " model vdw 2.286 2.520 ... (remaining 144708 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 193 through 751 or resid 801)) selection = (chain 'B' and (resid 193 through 237 or resid 243 through 751 or resid 801)) selection = (chain 'C' and (resid 193 through 237 or resid 243 through 751 or resid 801)) selection = (chain 'D' and (resid 193 through 751 or resid 801)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 1 through 74 or (resid 75 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or resid 901)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.620 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 46.370 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 19252 Z= 0.247 Angle : 0.716 13.972 26027 Z= 0.367 Chirality : 0.266 5.036 2901 Planarity : 0.003 0.037 3205 Dihedral : 13.416 177.947 7086 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.68 % Favored : 95.19 % Rotamer: Outliers : 0.15 % Allowed : 1.14 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.18), residues: 2266 helix: 1.78 (0.15), residues: 1252 sheet: -1.20 (0.61), residues: 71 loop : -1.17 (0.20), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 749 HIS 0.003 0.001 HIS C 206 PHE 0.025 0.002 PHE A 712 TYR 0.016 0.001 TYR B 565 ARG 0.003 0.000 ARG D 363 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 456 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 592 SER cc_start: 0.8803 (t) cc_final: 0.8567 (m) REVERT: F 10 SER cc_start: 0.8752 (m) cc_final: 0.8368 (p) REVERT: B 312 ILE cc_start: 0.8938 (mt) cc_final: 0.8593 (mp) REVERT: B 552 MET cc_start: 0.8601 (ttm) cc_final: 0.8249 (ttm) REVERT: B 571 LYS cc_start: 0.7481 (tptt) cc_final: 0.7118 (tttp) REVERT: B 651 GLU cc_start: 0.7485 (mm-30) cc_final: 0.7276 (mp0) REVERT: C 312 ILE cc_start: 0.9012 (mt) cc_final: 0.8727 (mt) REVERT: C 510 SER cc_start: 0.8307 (m) cc_final: 0.7959 (p) REVERT: D 234 ASP cc_start: 0.8112 (m-30) cc_final: 0.7811 (m-30) REVERT: D 398 VAL cc_start: 0.9413 (p) cc_final: 0.9193 (m) REVERT: D 743 ARG cc_start: 0.7745 (ttm110) cc_final: 0.7451 (ttm110) outliers start: 3 outliers final: 1 residues processed: 457 average time/residue: 0.3247 time to fit residues: 217.8905 Evaluate side-chains 290 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 289 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 190 optimal weight: 7.9990 chunk 171 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 205 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN E 20 ASN E 43 ASN B 289 HIS ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 691 GLN ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 HIS D 676 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19252 Z= 0.325 Angle : 0.627 11.442 26027 Z= 0.320 Chirality : 0.045 0.448 2901 Planarity : 0.004 0.064 3205 Dihedral : 14.161 173.503 2752 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.25 % Favored : 94.57 % Rotamer: Outliers : 2.08 % Allowed : 6.04 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2266 helix: 1.64 (0.15), residues: 1245 sheet: -1.58 (0.61), residues: 73 loop : -1.24 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 740 HIS 0.004 0.001 HIS A 410 PHE 0.020 0.002 PHE C 438 TYR 0.017 0.002 TYR D 487 ARG 0.005 0.001 ARG D 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 299 time to evaluate : 1.901 Fit side-chains revert: symmetry clash REVERT: A 428 ARG cc_start: 0.7323 (ttm-80) cc_final: 0.6978 (ttm-80) REVERT: A 592 SER cc_start: 0.8786 (t) cc_final: 0.8521 (m) REVERT: F 10 SER cc_start: 0.8660 (m) cc_final: 0.8367 (p) REVERT: B 571 LYS cc_start: 0.7469 (tptt) cc_final: 0.7128 (tttp) REVERT: B 574 LEU cc_start: 0.8124 (mm) cc_final: 0.7890 (mt) REVERT: C 445 MET cc_start: 0.9239 (mmp) cc_final: 0.8942 (mmp) REVERT: C 510 SER cc_start: 0.8211 (m) cc_final: 0.7589 (p) REVERT: D 234 ASP cc_start: 0.8175 (m-30) cc_final: 0.7833 (m-30) REVERT: D 398 VAL cc_start: 0.9410 (p) cc_final: 0.9186 (m) REVERT: D 743 ARG cc_start: 0.7806 (ttm110) cc_final: 0.7535 (ttm110) outliers start: 42 outliers final: 32 residues processed: 325 average time/residue: 0.2937 time to fit residues: 146.5287 Evaluate side-chains 304 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 272 time to evaluate : 2.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 393 ASN Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 650 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 170 optimal weight: 9.9990 chunk 139 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 222 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 203 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 628 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 206 HIS ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 19252 Z= 0.367 Angle : 0.626 8.221 26027 Z= 0.323 Chirality : 0.045 0.528 2901 Planarity : 0.004 0.063 3205 Dihedral : 13.529 172.048 2752 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.31 % Favored : 93.51 % Rotamer: Outliers : 2.77 % Allowed : 7.17 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2266 helix: 1.39 (0.15), residues: 1254 sheet: -1.79 (0.60), residues: 73 loop : -1.38 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 740 HIS 0.005 0.001 HIS B 358 PHE 0.023 0.002 PHE C 438 TYR 0.019 0.002 TYR B 453 ARG 0.006 0.001 ARG D 331 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 290 time to evaluate : 2.026 Fit side-chains revert: symmetry clash REVERT: A 428 ARG cc_start: 0.7298 (ttm-80) cc_final: 0.6872 (mtm-85) REVERT: F 10 SER cc_start: 0.8604 (m) cc_final: 0.8343 (p) REVERT: F 65 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8565 (tt) REVERT: B 571 LYS cc_start: 0.7509 (tptt) cc_final: 0.7092 (tttp) REVERT: B 651 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7389 (mp0) REVERT: C 510 SER cc_start: 0.8221 (m) cc_final: 0.7948 (p) REVERT: D 234 ASP cc_start: 0.8165 (m-30) cc_final: 0.7797 (m-30) REVERT: D 398 VAL cc_start: 0.9389 (p) cc_final: 0.9126 (m) outliers start: 56 outliers final: 43 residues processed: 325 average time/residue: 0.2843 time to fit residues: 142.8812 Evaluate side-chains 316 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 272 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 411 ASP Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 586 VAL Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 61 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 493 ILE Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 581 MET Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 494 GLN Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 390 CYS Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 722 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 203 optimal weight: 7.9990 chunk 154 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 98 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 206 optimal weight: 0.6980 chunk 218 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19252 Z= 0.135 Angle : 0.496 7.858 26027 Z= 0.262 Chirality : 0.040 0.493 2901 Planarity : 0.003 0.062 3205 Dihedral : 12.552 174.567 2752 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.00 % Favored : 93.91 % Rotamer: Outliers : 1.63 % Allowed : 9.65 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.18), residues: 2266 helix: 1.95 (0.15), residues: 1246 sheet: -1.88 (0.58), residues: 73 loop : -1.37 (0.20), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 740 HIS 0.002 0.000 HIS C 320 PHE 0.017 0.001 PHE A 712 TYR 0.016 0.001 TYR D 487 ARG 0.005 0.000 ARG D 331 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 300 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 65 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8482 (tt) REVERT: B 651 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7424 (mp0) REVERT: C 510 SER cc_start: 0.8268 (m) cc_final: 0.7857 (p) REVERT: D 234 ASP cc_start: 0.8164 (m-30) cc_final: 0.7810 (m-30) REVERT: D 398 VAL cc_start: 0.9409 (p) cc_final: 0.9208 (m) outliers start: 33 outliers final: 21 residues processed: 320 average time/residue: 0.2854 time to fit residues: 141.3356 Evaluate side-chains 285 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 263 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 493 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 181 optimal weight: 2.9990 chunk 124 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 186 optimal weight: 7.9990 chunk 151 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 111 optimal weight: 0.5980 chunk 196 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 676 ASN ** 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: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19252 Z= 0.262 Angle : 0.557 7.683 26027 Z= 0.288 Chirality : 0.042 0.455 2901 Planarity : 0.004 0.061 3205 Dihedral : 12.046 175.580 2752 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.71 % Favored : 93.12 % Rotamer: Outliers : 2.82 % Allowed : 9.45 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.18), residues: 2266 helix: 1.75 (0.15), residues: 1243 sheet: -1.86 (0.58), residues: 73 loop : -1.46 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 740 HIS 0.003 0.001 HIS B 358 PHE 0.017 0.002 PHE D 587 TYR 0.015 0.002 TYR B 453 ARG 0.005 0.000 ARG D 331 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 278 time to evaluate : 2.178 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 553 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8596 (mp) REVERT: F 65 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8548 (tt) REVERT: B 716 MET cc_start: 0.4768 (mmt) cc_final: 0.3572 (mmm) REVERT: C 510 SER cc_start: 0.8318 (m) cc_final: 0.7958 (p) REVERT: D 234 ASP cc_start: 0.8172 (m-30) cc_final: 0.7802 (m-30) REVERT: D 398 VAL cc_start: 0.9377 (p) cc_final: 0.9127 (m) outliers start: 57 outliers final: 40 residues processed: 313 average time/residue: 0.2828 time to fit residues: 137.9314 Evaluate side-chains 312 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 270 time to evaluate : 1.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 329 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 494 GLN Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 670 THR Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 553 LEU Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 654 ASP Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 650 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 73 optimal weight: 9.9990 chunk 196 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 128 optimal weight: 0.0970 chunk 53 optimal weight: 7.9990 chunk 218 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 101 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 72 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 HIS B 628 ASN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19252 Z= 0.187 Angle : 0.511 7.758 26027 Z= 0.267 Chirality : 0.040 0.423 2901 Planarity : 0.003 0.062 3205 Dihedral : 11.413 162.237 2752 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.53 % Favored : 93.38 % Rotamer: Outliers : 2.23 % Allowed : 10.69 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 2266 helix: 1.89 (0.15), residues: 1241 sheet: -1.81 (0.58), residues: 73 loop : -1.49 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 740 HIS 0.002 0.001 HIS D 358 PHE 0.015 0.001 PHE A 712 TYR 0.013 0.001 TYR C 351 ARG 0.008 0.000 ARG D 331 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 273 time to evaluate : 1.864 Fit side-chains revert: symmetry clash REVERT: F 65 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8551 (tt) REVERT: B 571 LYS cc_start: 0.7127 (tttp) cc_final: 0.6878 (mmpt) REVERT: C 510 SER cc_start: 0.8334 (m) cc_final: 0.7908 (p) REVERT: D 234 ASP cc_start: 0.8169 (m-30) cc_final: 0.7804 (m-30) REVERT: D 359 GLU cc_start: 0.8058 (tp30) cc_final: 0.7852 (tp30) REVERT: D 398 VAL cc_start: 0.9399 (p) cc_final: 0.9162 (m) outliers start: 45 outliers final: 36 residues processed: 299 average time/residue: 0.2898 time to fit residues: 133.7675 Evaluate side-chains 300 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 263 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 509 ASP Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 562 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 210 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 124 optimal weight: 20.0000 chunk 159 optimal weight: 1.9990 chunk 123 optimal weight: 8.9990 chunk 184 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 217 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 19252 Z= 0.187 Angle : 0.509 7.679 26027 Z= 0.265 Chirality : 0.040 0.401 2901 Planarity : 0.003 0.063 3205 Dihedral : 10.757 138.229 2752 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.93 % Favored : 92.98 % Rotamer: Outliers : 2.33 % Allowed : 10.89 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.18), residues: 2266 helix: 1.88 (0.15), residues: 1248 sheet: -1.79 (0.58), residues: 73 loop : -1.48 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 372 HIS 0.002 0.001 HIS A 289 PHE 0.015 0.001 PHE A 712 TYR 0.015 0.001 TYR C 351 ARG 0.005 0.000 ARG D 331 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 273 time to evaluate : 1.937 Fit side-chains revert: symmetry clash REVERT: F 65 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8552 (tt) REVERT: B 571 LYS cc_start: 0.7216 (tttp) cc_final: 0.6940 (mmpt) REVERT: B 716 MET cc_start: 0.4969 (mmt) cc_final: 0.3750 (mmm) REVERT: C 510 SER cc_start: 0.8345 (m) cc_final: 0.7907 (p) REVERT: D 234 ASP cc_start: 0.8181 (m-30) cc_final: 0.7818 (m-30) REVERT: D 359 GLU cc_start: 0.8161 (tp30) cc_final: 0.7902 (tp30) REVERT: D 398 VAL cc_start: 0.9414 (p) cc_final: 0.9178 (m) outliers start: 47 outliers final: 34 residues processed: 297 average time/residue: 0.3049 time to fit residues: 140.3647 Evaluate side-chains 297 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 262 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 72 GLU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 722 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 134 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 138 optimal weight: 0.2980 chunk 148 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 171 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19252 Z= 0.170 Angle : 0.499 7.605 26027 Z= 0.260 Chirality : 0.040 0.382 2901 Planarity : 0.003 0.064 3205 Dihedral : 10.255 112.791 2752 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.75 % Favored : 93.20 % Rotamer: Outliers : 2.13 % Allowed : 11.08 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2266 helix: 1.95 (0.15), residues: 1249 sheet: -1.77 (0.58), residues: 73 loop : -1.46 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 372 HIS 0.002 0.001 HIS A 289 PHE 0.020 0.001 PHE B 369 TYR 0.015 0.001 TYR C 351 ARG 0.005 0.000 ARG D 331 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 267 time to evaluate : 1.927 Fit side-chains revert: symmetry clash REVERT: A 413 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8740 (tt) REVERT: A 553 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8572 (mp) REVERT: F 65 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8562 (tt) REVERT: B 571 LYS cc_start: 0.7198 (tttp) cc_final: 0.6928 (mmpt) REVERT: B 716 MET cc_start: 0.5038 (mmt) cc_final: 0.3693 (mmm) REVERT: C 510 SER cc_start: 0.8329 (m) cc_final: 0.7900 (p) REVERT: D 234 ASP cc_start: 0.8182 (m-30) cc_final: 0.7822 (m-30) REVERT: D 359 GLU cc_start: 0.8224 (tp30) cc_final: 0.7964 (tp30) REVERT: D 398 VAL cc_start: 0.9404 (p) cc_final: 0.9187 (m) outliers start: 43 outliers final: 33 residues processed: 289 average time/residue: 0.2852 time to fit residues: 127.1350 Evaluate side-chains 297 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 261 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 722 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 208 optimal weight: 0.7980 chunk 190 optimal weight: 9.9990 chunk 202 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 183 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19252 Z= 0.201 Angle : 0.513 7.652 26027 Z= 0.266 Chirality : 0.040 0.382 2901 Planarity : 0.003 0.066 3205 Dihedral : 10.041 109.153 2752 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.33 % Favored : 92.63 % Rotamer: Outliers : 2.38 % Allowed : 10.94 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2266 helix: 1.85 (0.15), residues: 1261 sheet: -1.78 (0.58), residues: 73 loop : -1.52 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 372 HIS 0.002 0.001 HIS A 289 PHE 0.023 0.001 PHE D 247 TYR 0.016 0.001 TYR C 351 ARG 0.006 0.000 ARG D 331 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 265 time to evaluate : 1.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 413 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8745 (tt) REVERT: A 553 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8586 (mp) REVERT: F 65 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8562 (tt) REVERT: B 571 LYS cc_start: 0.7202 (tttp) cc_final: 0.6924 (mmpt) REVERT: B 716 MET cc_start: 0.4959 (OUTLIER) cc_final: 0.3629 (mmm) REVERT: D 212 ARG cc_start: 0.7509 (mtp85) cc_final: 0.7244 (mtp85) REVERT: D 234 ASP cc_start: 0.8182 (m-30) cc_final: 0.7824 (m-30) REVERT: D 359 GLU cc_start: 0.8300 (tp30) cc_final: 0.8026 (tp30) REVERT: D 398 VAL cc_start: 0.9407 (p) cc_final: 0.9178 (m) REVERT: D 628 ASN cc_start: 0.7788 (t0) cc_final: 0.7506 (t0) outliers start: 48 outliers final: 40 residues processed: 290 average time/residue: 0.2916 time to fit residues: 130.5978 Evaluate side-chains 308 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 264 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 592 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain F residue 25 MET Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 572 MET Chi-restraints excluded: chain C residue 578 CYS Chi-restraints excluded: chain C residue 592 SER Chi-restraints excluded: chain C residue 644 MET Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 335 THR Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 562 MET Chi-restraints excluded: chain D residue 650 THR Chi-restraints excluded: chain D residue 722 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 131 optimal weight: 5.9990 chunk 101 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 179 optimal weight: 3.9990 chunk 18 optimal weight: 0.0870 chunk 138 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 142 optimal weight: 0.9980 chunk 190 optimal weight: 10.0000 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 628 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 19252 Z= 0.150 Angle : 0.491 7.580 26027 Z= 0.257 Chirality : 0.039 0.371 2901 Planarity : 0.003 0.066 3205 Dihedral : 9.590 109.633 2752 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.62 % Favored : 93.34 % Rotamer: Outliers : 1.68 % Allowed : 11.73 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.19), residues: 2266 helix: 2.03 (0.15), residues: 1258 sheet: -1.82 (0.58), residues: 73 loop : -1.50 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 372 HIS 0.002 0.000 HIS A 289 PHE 0.022 0.001 PHE D 247 TYR 0.015 0.001 TYR C 351 ARG 0.005 0.000 ARG D 331 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4532 Ramachandran restraints generated. 2266 Oldfield, 0 Emsley, 2266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 277 time to evaluate : 2.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 553 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8574 (mp) REVERT: F 65 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8563 (tt) REVERT: B 571 LYS cc_start: 0.7194 (tttp) cc_final: 0.6898 (mmpt) REVERT: B 716 MET cc_start: 0.5009 (OUTLIER) cc_final: 0.4003 (mmm) REVERT: C 510 SER cc_start: 0.8266 (m) cc_final: 0.7818 (p) REVERT: D 234 ASP cc_start: 0.8180 (m-30) cc_final: 0.7828 (m-30) REVERT: D 359 GLU cc_start: 0.8318 (tp30) cc_final: 0.8028 (tp30) REVERT: D 398 VAL cc_start: 0.9404 (p) cc_final: 0.9197 (m) outliers start: 34 outliers final: 29 residues processed: 293 average time/residue: 0.2935 time to fit residues: 133.4821 Evaluate side-chains 300 residues out of total 2021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 268 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 304 PHE Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 553 LEU Chi-restraints excluded: chain A residue 561 GLN Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain B residue 287 VAL Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 390 CYS Chi-restraints excluded: chain B residue 393 ASN Chi-restraints excluded: chain B residue 404 SER Chi-restraints excluded: chain B residue 547 MET Chi-restraints excluded: chain B residue 568 MET Chi-restraints excluded: chain B residue 572 MET Chi-restraints excluded: chain B residue 644 MET Chi-restraints excluded: chain B residue 716 MET Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 377 VAL Chi-restraints excluded: chain C residue 393 ASN Chi-restraints excluded: chain C residue 445 MET Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 319 LEU Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 393 ASN Chi-restraints excluded: chain D residue 394 SER Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 572 MET Chi-restraints excluded: chain D residue 650 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 54 optimal weight: 1.9990 chunk 165 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 49 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 chunk 75 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 676 ASN ** 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 = 0.4060 r_free = 0.4060 target = 0.196883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.147316 restraints weight = 20576.431| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 1.84 r_work: 0.3173 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 19252 Z= 0.155 Angle : 0.501 8.035 26027 Z= 0.260 Chirality : 0.039 0.370 2901 Planarity : 0.003 0.066 3205 Dihedral : 9.456 109.483 2752 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.84 % Favored : 93.12 % Rotamer: Outliers : 1.78 % Allowed : 11.88 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.15 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.19), residues: 2266 helix: 2.03 (0.15), residues: 1257 sheet: -1.75 (0.58), residues: 73 loop : -1.50 (0.20), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 740 HIS 0.002 0.001 HIS A 289 PHE 0.029 0.001 PHE D 247 TYR 0.037 0.001 TYR D 309 ARG 0.005 0.000 ARG D 331 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3777.83 seconds wall clock time: 69 minutes 5.37 seconds (4145.37 seconds total)