Starting phenix.real_space_refine on Tue Dec 12 10:12:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqc_21348/12_2023/6vqc_21348.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqc_21348/12_2023/6vqc_21348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqc_21348/12_2023/6vqc_21348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqc_21348/12_2023/6vqc_21348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqc_21348/12_2023/6vqc_21348.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vqc_21348/12_2023/6vqc_21348.pdb" } resolution = 3.8 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= -0.002 sd= 0.069 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: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 13770 2.51 5 N 3384 2.21 5 O 3702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 388": "OE1" <-> "OE2" Residue "a TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 468": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 563": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 571": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 598": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 621": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 630": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 780": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 821": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 828": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 431": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 20991 Number of models: 1 Model: "" Number of chains: 18 Chain: "H" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 803 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 1, 'TRANS': 102} Chain: "L" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "a" Number of atoms: 3495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3495 Classifications: {'peptide': 441} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 18, 'TRANS': 422} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "b" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "c" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "d" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2833 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain: "e" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 621 Classifications: {'peptide': 78} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 71} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "f" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 480 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 3, 'TRANS': 80} Chain breaks: 1 Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "g" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "p" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 432 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Time building chain proxies: 11.31, per 1000 atoms: 0.54 Number of scatterers: 20991 At special positions: 0 Unit cell: (119.78, 125.08, 164.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 135 16.00 O 3702 8.00 N 3384 7.00 C 13770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.21 Conformation dependent library (CDL) restraints added in 4.1 seconds 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5030 Finding SS restraints... Secondary structure from input PDB file: 117 helices and 3 sheets defined 81.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.68 Creating SS restraints... Processing helix chain 'H' and resid 50 through 77 Processing helix chain 'H' and resid 79 through 86 Processing helix chain 'H' and resid 127 through 153 removed outlier: 3.706A pdb=" N THR H 153 " --> pdb=" O ALA H 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 13 through 23 Processing helix chain 'L' and resid 44 through 57 Processing helix chain 'L' and resid 68 through 74 Processing helix chain 'L' and resid 75 through 81 removed outlier: 4.026A pdb=" N HIS L 81 " --> pdb=" O ALA L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 109 Processing helix chain 'a' and resid 370 through 380 removed outlier: 4.481A pdb=" N PHE a 374 " --> pdb=" O PHE a 370 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 407 removed outlier: 4.707A pdb=" N ILE a 397 " --> pdb=" O PRO a 393 " (cutoff:3.500A) Proline residue: a 400 - end of helix Processing helix chain 'a' and resid 409 through 426 Processing helix chain 'a' and resid 426 through 432 Processing helix chain 'a' and resid 437 through 446 Processing helix chain 'a' and resid 446 through 465 removed outlier: 3.535A pdb=" N LEU a 452 " --> pdb=" O TYR a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 481 through 488 removed outlier: 3.559A pdb=" N ILE a 487 " --> pdb=" O PRO a 483 " (cutoff:3.500A) Processing helix chain 'a' and resid 495 through 500 Processing helix chain 'a' and resid 520 through 526 Processing helix chain 'a' and resid 528 through 563 removed outlier: 4.344A pdb=" N ASN a 534 " --> pdb=" O LEU a 530 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE a 536 " --> pdb=" O PHE a 532 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER a 556 " --> pdb=" O GLY a 552 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU a 557 " --> pdb=" O VAL a 553 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE a 558 " --> pdb=" O SER a 554 " (cutoff:3.500A) Processing helix chain 'a' and resid 565 through 571 removed outlier: 3.604A pdb=" N ILE a 569 " --> pdb=" O LYS a 565 " (cutoff:3.500A) Processing helix chain 'a' and resid 572 through 598 removed outlier: 4.398A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU a 587 " --> pdb=" O LEU a 583 " (cutoff:3.500A) Processing helix chain 'a' and resid 599 through 603 Processing helix chain 'a' and resid 608 through 619 Processing helix chain 'a' and resid 632 through 667 removed outlier: 3.685A pdb=" N VAL a 648 " --> pdb=" O ALA a 644 " (cutoff:3.500A) Proline residue: a 649 - end of helix removed outlier: 5.906A pdb=" N LYS a 655 " --> pdb=" O MET a 651 " (cutoff:3.500A) Proline residue: a 656 - end of helix Processing helix chain 'a' and resid 713 through 739 Processing helix chain 'a' and resid 739 through 759 removed outlier: 4.234A pdb=" N TRP a 743 " --> pdb=" O TYR a 739 " (cutoff:3.500A) Processing helix chain 'a' and resid 761 through 765 Processing helix chain 'a' and resid 768 through 791 Processing helix chain 'a' and resid 793 through 810 Processing helix chain 'a' and resid 811 through 815 Processing helix chain 'b' and resid 3 through 29 Processing helix chain 'b' and resid 36 through 44 Processing helix chain 'b' and resid 45 through 80 removed outlier: 3.712A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER b 75 " --> pdb=" O ILE b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 81 through 82 No H-bonds generated for 'chain 'b' and resid 81 through 82' Processing helix chain 'b' and resid 83 through 84 No H-bonds generated for 'chain 'b' and resid 83 through 84' Processing helix chain 'b' and resid 85 through 90 removed outlier: 4.228A pdb=" N LYS b 89 " --> pdb=" O ARG b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 113 removed outlier: 3.748A pdb=" N GLY b 104 " --> pdb=" O VAL b 100 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 169 removed outlier: 3.883A pdb=" N GLN b 168 " --> pdb=" O LEU b 164 " (cutoff:3.500A) Processing helix chain 'b' and resid 172 through 198 removed outlier: 4.090A pdb=" N ILE b 178 " --> pdb=" O VAL b 174 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL b 179 " --> pdb=" O LYS b 175 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU b 180 " --> pdb=" O ILE b 176 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY b 187 " --> pdb=" O GLY b 183 " (cutoff:3.500A) Processing helix chain 'c' and resid 416 through 442 Processing helix chain 'd' and resid 8 through 25 removed outlier: 4.199A pdb=" N ASP d 12 " --> pdb=" O TYR d 8 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TYR d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU d 16 " --> pdb=" O ASP d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 38 Processing helix chain 'd' and resid 41 through 50 Processing helix chain 'd' and resid 66 through 88 Processing helix chain 'd' and resid 90 through 116 removed outlier: 4.823A pdb=" N PHE d 96 " --> pdb=" O PRO d 92 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE d 100 " --> pdb=" O PHE d 96 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR d 114 " --> pdb=" O ILE d 110 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY d 115 " --> pdb=" O LEU d 111 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 126 Processing helix chain 'd' and resid 127 through 129 No H-bonds generated for 'chain 'd' and resid 127 through 129' Processing helix chain 'd' and resid 146 through 158 Processing helix chain 'd' and resid 159 through 167 removed outlier: 4.179A pdb=" N ALA d 162 " --> pdb=" O PRO d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 176 Processing helix chain 'd' and resid 177 through 200 Processing helix chain 'd' and resid 202 through 227 Proline residue: d 210 - end of helix Processing helix chain 'd' and resid 228 through 230 No H-bonds generated for 'chain 'd' and resid 228 through 230' Processing helix chain 'd' and resid 233 through 239 Processing helix chain 'd' and resid 251 through 258 Processing helix chain 'd' and resid 260 through 269 Processing helix chain 'd' and resid 271 through 281 removed outlier: 4.408A pdb=" N LEU d 277 " --> pdb=" O GLU d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 305 Processing helix chain 'd' and resid 306 through 308 No H-bonds generated for 'chain 'd' and resid 306 through 308' Processing helix chain 'd' and resid 312 through 338 removed outlier: 3.710A pdb=" N TYR d 316 " --> pdb=" O PHE d 312 " (cutoff:3.500A) Processing helix chain 'd' and resid 340 through 344 Processing helix chain 'e' and resid 6 through 23 Processing helix chain 'e' and resid 24 through 27 Processing helix chain 'e' and resid 33 through 58 Processing helix chain 'e' and resid 69 through 78 Processing helix chain 'f' and resid 8 through 36 Processing helix chain 'f' and resid 54 through 90 removed outlier: 4.094A pdb=" N ILE f 58 " --> pdb=" O GLY f 54 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 46 removed outlier: 3.726A pdb=" N PHE g 14 " --> pdb=" O TYR g 10 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER g 26 " --> pdb=" O ALA g 22 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VAL g 46 " --> pdb=" O ALA g 42 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 52 Processing helix chain 'g' and resid 53 through 55 No H-bonds generated for 'chain 'g' and resid 53 through 55' Processing helix chain 'g' and resid 56 through 78 Processing helix chain 'g' and resid 86 through 124 Processing helix chain 'g' and resid 127 through 153 Processing helix chain 'h' and resid 11 through 46 removed outlier: 4.573A pdb=" N GLY h 15 " --> pdb=" O SER h 11 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET h 23 " --> pdb=" O ALA h 19 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL h 46 " --> pdb=" O ALA h 42 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 52 Processing helix chain 'h' and resid 56 through 78 Processing helix chain 'h' and resid 86 through 124 Processing helix chain 'h' and resid 127 through 154 removed outlier: 3.531A pdb=" N GLY h 145 " --> pdb=" O LEU h 141 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR h 154 " --> pdb=" O LEU h 150 " (cutoff:3.500A) Processing helix chain 'i' and resid 10 through 48 removed outlier: 4.120A pdb=" N PHE i 14 " --> pdb=" O TYR i 10 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY i 15 " --> pdb=" O SER i 11 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET i 23 " --> pdb=" O ALA i 19 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 52 Processing helix chain 'i' and resid 56 through 78 Processing helix chain 'i' and resid 86 through 124 removed outlier: 3.936A pdb=" N GLN i 123 " --> pdb=" O ARG i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 154 removed outlier: 4.643A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY i 145 " --> pdb=" O LEU i 141 " (cutoff:3.500A) Processing helix chain 'j' and resid 11 through 45 removed outlier: 4.336A pdb=" N GLY j 15 " --> pdb=" O SER j 11 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET j 23 " --> pdb=" O ALA j 19 " (cutoff:3.500A) Processing helix chain 'j' and resid 48 through 52 Processing helix chain 'j' and resid 53 through 55 No H-bonds generated for 'chain 'j' and resid 53 through 55' Processing helix chain 'j' and resid 56 through 78 removed outlier: 4.071A pdb=" N ILE j 64 " --> pdb=" O VAL j 60 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE j 65 " --> pdb=" O MET j 61 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ALA j 66 " --> pdb=" O ALA j 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 86 through 124 Processing helix chain 'j' and resid 126 through 154 removed outlier: 4.661A pdb=" N GLY j 130 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY j 142 " --> pdb=" O ALA j 138 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 48 removed outlier: 4.172A pdb=" N PHE k 14 " --> pdb=" O TYR k 10 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY k 15 " --> pdb=" O SER k 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET k 23 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N VAL k 46 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET k 47 " --> pdb=" O ALA k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 52 Processing helix chain 'k' and resid 53 through 55 No H-bonds generated for 'chain 'k' and resid 53 through 55' Processing helix chain 'k' and resid 56 through 80 Processing helix chain 'k' and resid 86 through 124 Processing helix chain 'k' and resid 127 through 154 Processing helix chain 'l' and resid 11 through 48 removed outlier: 4.473A pdb=" N GLY l 15 " --> pdb=" O SER l 11 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL l 46 " --> pdb=" O ALA l 42 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET l 47 " --> pdb=" O ALA l 43 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 55 removed outlier: 3.925A pdb=" N MET l 53 " --> pdb=" O GLU l 50 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 80 Processing helix chain 'l' and resid 86 through 124 removed outlier: 3.932A pdb=" N GLN l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) Processing helix chain 'l' and resid 126 through 155 removed outlier: 4.231A pdb=" N GLY l 130 " --> pdb=" O ARG l 126 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 45 removed outlier: 4.068A pdb=" N PHE m 14 " --> pdb=" O TYR m 10 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER m 26 " --> pdb=" O ALA m 22 " (cutoff:3.500A) Processing helix chain 'm' and resid 46 through 47 No H-bonds generated for 'chain 'm' and resid 46 through 47' Processing helix chain 'm' and resid 48 through 55 removed outlier: 4.799A pdb=" N MET m 53 " --> pdb=" O GLU m 50 " (cutoff:3.500A) Processing helix chain 'm' and resid 56 through 80 Processing helix chain 'm' and resid 86 through 124 removed outlier: 3.986A pdb=" N GLN m 123 " --> pdb=" O ARG m 119 " (cutoff:3.500A) Processing helix chain 'm' and resid 126 through 154 removed outlier: 4.364A pdb=" N GLY m 130 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY m 145 " --> pdb=" O LEU m 141 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR m 154 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 46 removed outlier: 4.316A pdb=" N PHE n 14 " --> pdb=" O TYR n 10 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY n 15 " --> pdb=" O SER n 11 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL n 46 " --> pdb=" O ALA n 42 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 52 Processing helix chain 'n' and resid 56 through 79 Processing helix chain 'n' and resid 86 through 123 removed outlier: 3.624A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 126 through 154 removed outlier: 4.651A pdb=" N GLY n 130 " --> pdb=" O ARG n 126 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY n 145 " --> pdb=" O LEU n 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR n 154 " --> pdb=" O LEU n 150 " (cutoff:3.500A) Processing helix chain 'o' and resid 11 through 48 removed outlier: 4.357A pdb=" N GLY o 15 " --> pdb=" O SER o 11 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N MET o 47 " --> pdb=" O ALA o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 51 through 56 Processing helix chain 'o' and resid 56 through 80 removed outlier: 3.503A pdb=" N VAL o 60 " --> pdb=" O ILE o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 86 through 124 Processing helix chain 'o' and resid 127 through 154 removed outlier: 3.577A pdb=" N GLY o 145 " --> pdb=" O LEU o 141 " (cutoff:3.500A) Processing helix chain 'p' and resid 302 through 330 Processing helix chain 'p' and resid 338 through 343 Processing sheet with id=AA1, first strand: chain 'H' and resid 93 through 99 Processing sheet with id=AA2, first strand: chain 'L' and resid 36 through 38 removed outlier: 8.520A pdb=" N LEU L 37 " --> pdb=" O ILE L 8 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL L 10 " --> pdb=" O LEU L 37 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA L 9 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N ASN L 67 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ILE L 11 " --> pdb=" O ASN L 67 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE L 64 " --> pdb=" O LEU L 89 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N ILE L 91 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE L 66 " --> pdb=" O ILE L 91 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'a' and resid 362 through 363 1747 hydrogen bonds defined for protein. 5121 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: 7.22 Time building geometry restraints manager: 9.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3288 1.30 - 1.43: 5515 1.43 - 1.55: 12361 1.55 - 1.68: 0 1.68 - 1.81: 250 Bond restraints: 21414 Sorted by residual: bond pdb=" C PRO H 107 " pdb=" O PRO H 107 " ideal model delta sigma weight residual 1.233 1.171 0.062 9.60e-03 1.09e+04 4.15e+01 bond pdb=" N PRO L 86 " pdb=" CD PRO L 86 " ideal model delta sigma weight residual 1.473 1.536 -0.063 1.40e-02 5.10e+03 2.04e+01 bond pdb=" CA ALA H 102 " pdb=" CB ALA H 102 " ideal model delta sigma weight residual 1.542 1.503 0.039 8.90e-03 1.26e+04 1.94e+01 bond pdb=" CA ALA L 109 " pdb=" CB ALA L 109 " ideal model delta sigma weight residual 1.529 1.474 0.055 1.34e-02 5.57e+03 1.68e+01 bond pdb=" N PRO g 8 " pdb=" CD PRO g 8 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.67e+01 ... (remaining 21409 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.41: 563 106.41 - 113.27: 11718 113.27 - 120.14: 8419 120.14 - 127.01: 8152 127.01 - 133.88: 173 Bond angle restraints: 29025 Sorted by residual: angle pdb=" N GLN d 171 " pdb=" CA GLN d 171 " pdb=" C GLN d 171 " ideal model delta sigma weight residual 111.28 102.54 8.74 1.09e+00 8.42e-01 6.43e+01 angle pdb=" C ARG L 108 " pdb=" N ALA L 109 " pdb=" CA ALA L 109 " ideal model delta sigma weight residual 122.77 112.35 10.42 1.33e+00 5.65e-01 6.14e+01 angle pdb=" N SER L 104 " pdb=" CA SER L 104 " pdb=" C SER L 104 " ideal model delta sigma weight residual 111.36 103.07 8.29 1.09e+00 8.42e-01 5.79e+01 angle pdb=" C ILE L 91 " pdb=" N PRO L 92 " pdb=" CA PRO L 92 " ideal model delta sigma weight residual 119.83 127.73 -7.90 1.08e+00 8.57e-01 5.35e+01 angle pdb=" C ASN m 7 " pdb=" N PRO m 8 " pdb=" CA PRO m 8 " ideal model delta sigma weight residual 119.90 127.30 -7.40 1.05e+00 9.07e-01 4.97e+01 ... (remaining 29020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11995 17.95 - 35.90: 331 35.90 - 53.85: 84 53.85 - 71.80: 21 71.80 - 89.75: 23 Dihedral angle restraints: 12454 sinusoidal: 4528 harmonic: 7926 Sorted by residual: dihedral pdb=" CA ILE a 793 " pdb=" C ILE a 793 " pdb=" N MET a 794 " pdb=" CA MET a 794 " ideal model delta harmonic sigma weight residual -180.00 -159.91 -20.09 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLN d 119 " pdb=" C GLN d 119 " pdb=" N ARG d 120 " pdb=" CA ARG d 120 " ideal model delta harmonic sigma weight residual 180.00 160.21 19.79 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" CA GLU l 50 " pdb=" C GLU l 50 " pdb=" N LEU l 51 " pdb=" CA LEU l 51 " ideal model delta harmonic sigma weight residual -180.00 -162.54 -17.46 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 12451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2307 0.060 - 0.120: 917 0.120 - 0.180: 124 0.180 - 0.240: 75 0.240 - 0.300: 11 Chirality restraints: 3434 Sorted by residual: chirality pdb=" CA TYR n 68 " pdb=" N TYR n 68 " pdb=" C TYR n 68 " pdb=" CB TYR n 68 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA TYR g 144 " pdb=" N TYR g 144 " pdb=" C TYR g 144 " pdb=" CB TYR g 144 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" CA TYR l 68 " pdb=" N TYR l 68 " pdb=" C TYR l 68 " pdb=" CB TYR l 68 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 3431 not shown) Planarity restraints: 3606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU o 86 " 0.023 2.00e-02 2.50e+03 4.57e-02 2.09e+01 pdb=" C LEU o 86 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU o 86 " 0.029 2.00e-02 2.50e+03 pdb=" N TYR o 87 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN k 7 " -0.022 2.00e-02 2.50e+03 4.29e-02 1.84e+01 pdb=" C ASN k 7 " 0.074 2.00e-02 2.50e+03 pdb=" O ASN k 7 " -0.028 2.00e-02 2.50e+03 pdb=" N PRO k 8 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU d 160 " 0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C LEU d 160 " -0.069 2.00e-02 2.50e+03 pdb=" O LEU d 160 " 0.026 2.00e-02 2.50e+03 pdb=" N ALA d 161 " 0.023 2.00e-02 2.50e+03 ... (remaining 3603 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 6839 2.82 - 3.34: 23215 3.34 - 3.86: 35952 3.86 - 4.38: 43070 4.38 - 4.90: 69362 Nonbonded interactions: 178438 Sorted by model distance: nonbonded pdb=" OG SER b 136 " pdb=" O GLN b 197 " model vdw 2.305 2.440 nonbonded pdb=" NZ LYS H 55 " pdb=" OD2 ASP L 99 " model vdw 2.319 2.520 nonbonded pdb=" O GLU o 9 " pdb=" N SER o 11 " model vdw 2.372 2.520 nonbonded pdb=" O PRO i 8 " pdb=" OG SER i 11 " model vdw 2.373 2.440 nonbonded pdb=" O PRO d 249 " pdb=" NE2 GLN m 123 " model vdw 2.380 2.520 ... (remaining 178433 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 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } 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: 2.250 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: 9.570 Check model and map are aligned: 0.320 Set scattering table: 0.210 Process input model: 58.470 Find NCS groups from input model: 1.020 Set up NCS constraints: 0.150 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 : 0.008 0.063 21414 Z= 0.541 Angle : 0.964 10.419 29025 Z= 0.725 Chirality : 0.067 0.300 3434 Planarity : 0.005 0.046 3606 Dihedral : 11.016 89.754 7424 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.63 % Favored : 97.15 % Rotamer: Outliers : 0.61 % Allowed : 1.49 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.14), residues: 2771 helix: 1.05 (0.10), residues: 2047 sheet: -0.40 (1.07), residues: 18 loop : -1.34 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP a 743 HIS 0.001 0.000 HIS a 807 PHE 0.011 0.000 PHE i 128 TYR 0.011 0.001 TYR d 33 ARG 0.001 0.000 ARG l 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1256 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 1243 time to evaluate : 2.408 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: symmetry clash outliers start: 13 outliers final: 3 residues processed: 1249 average time/residue: 0.3059 time to fit residues: 595.9279 Evaluate side-chains 725 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 722 time to evaluate : 2.235 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2000 time to fit residues: 4.0232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 0.8980 chunk 211 optimal weight: 0.0000 chunk 117 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 chunk 142 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 132 optimal weight: 0.6980 chunk 162 optimal weight: 0.8980 chunk 253 optimal weight: 0.8980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 96 HIS a 433 GLN a 548 HIS ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS d 50 GLN d 119 GLN d 297 HIS ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 6 ASN j 78 ASN ** k 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 7 ASN m 78 ASN n 6 ASN p 294 ASN p 330 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.3832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 21414 Z= 0.248 Angle : 0.725 11.982 29025 Z= 0.378 Chirality : 0.044 0.306 3434 Planarity : 0.005 0.040 3606 Dihedral : 4.111 19.478 2978 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.45 % Favored : 97.51 % Rotamer: Outliers : 5.93 % Allowed : 18.15 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.15), residues: 2771 helix: 2.01 (0.10), residues: 2081 sheet: -0.79 (1.05), residues: 18 loop : -0.87 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP e 74 HIS 0.006 0.001 HIS b 132 PHE 0.041 0.002 PHE e 6 TYR 0.030 0.002 TYR h 144 ARG 0.006 0.001 ARG L 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 964 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 837 time to evaluate : 2.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 66 residues processed: 891 average time/residue: 0.3094 time to fit residues: 435.5856 Evaluate side-chains 745 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 679 time to evaluate : 2.491 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.2015 time to fit residues: 28.3152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 140 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 210 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 253 optimal weight: 0.7980 chunk 274 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 251 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 203 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 100 ASN L 33 HIS ** a 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 637 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 HIS ** d 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 78 ASN ** k 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 78 ASN ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 21414 Z= 0.262 Angle : 0.682 10.905 29025 Z= 0.358 Chirality : 0.042 0.291 3434 Planarity : 0.005 0.047 3606 Dihedral : 4.095 27.555 2978 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.50 % Allowed : 21.89 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.15), residues: 2771 helix: 1.93 (0.11), residues: 2083 sheet: -0.96 (1.06), residues: 18 loop : -0.97 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP e 74 HIS 0.005 0.001 HIS a 830 PHE 0.037 0.002 PHE j 13 TYR 0.035 0.002 TYR n 144 ARG 0.004 0.001 ARG H 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 735 time to evaluate : 2.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 43 residues processed: 773 average time/residue: 0.3093 time to fit residues: 377.0849 Evaluate side-chains 703 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 660 time to evaluate : 2.600 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.2096 time to fit residues: 19.6073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 250 optimal weight: 0.9980 chunk 190 optimal weight: 0.5980 chunk 131 optimal weight: 0.8980 chunk 28 optimal weight: 0.2980 chunk 121 optimal weight: 0.7980 chunk 170 optimal weight: 0.7980 chunk 254 optimal weight: 7.9990 chunk 269 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 241 optimal weight: 0.3980 chunk 72 optimal weight: 0.2980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 113 HIS ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 433 GLN a 633 GLN ** a 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 302 ASN ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 78 ASN k 7 ASN ** k 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 78 ASN ** m 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 21414 Z= 0.217 Angle : 0.661 10.249 29025 Z= 0.342 Chirality : 0.041 0.252 3434 Planarity : 0.004 0.039 3606 Dihedral : 4.089 22.488 2978 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.29 % Allowed : 23.89 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.15), residues: 2771 helix: 1.98 (0.11), residues: 2058 sheet: -1.03 (1.16), residues: 18 loop : -0.92 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP e 74 HIS 0.009 0.001 HIS a 807 PHE 0.041 0.002 PHE j 13 TYR 0.042 0.002 TYR n 144 ARG 0.010 0.001 ARG l 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 785 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 736 time to evaluate : 2.391 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 outliers start: 49 outliers final: 17 residues processed: 756 average time/residue: 0.3081 time to fit residues: 367.6048 Evaluate side-chains 672 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 655 time to evaluate : 2.426 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2063 time to fit residues: 9.7559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 224 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 230 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 chunk 242 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 HIS ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 735 ASN a 812 GLN ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 346 ASN ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 78 ASN ** m 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 21414 Z= 0.282 Angle : 0.686 12.259 29025 Z= 0.358 Chirality : 0.042 0.269 3434 Planarity : 0.004 0.045 3606 Dihedral : 4.076 18.693 2978 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.89 % Allowed : 25.71 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.16), residues: 2771 helix: 1.94 (0.11), residues: 2066 sheet: -1.21 (1.17), residues: 18 loop : -0.95 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP e 74 HIS 0.007 0.001 HIS L 81 PHE 0.038 0.002 PHE j 13 TYR 0.054 0.002 TYR i 144 ARG 0.007 0.001 ARG l 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 720 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 35 residues processed: 745 average time/residue: 0.3201 time to fit residues: 382.8580 Evaluate side-chains 688 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 653 time to evaluate : 2.388 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.1979 time to fit residues: 16.2432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 90 optimal weight: 0.8980 chunk 242 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 269 optimal weight: 0.9990 chunk 224 optimal weight: 0.7980 chunk 124 optimal weight: 0.0970 chunk 22 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 HIS L 96 HIS ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 92 GLN ** o 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 21414 Z= 0.227 Angle : 0.686 10.558 29025 Z= 0.354 Chirality : 0.042 0.274 3434 Planarity : 0.004 0.042 3606 Dihedral : 4.098 17.911 2978 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 16.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.05 % Allowed : 26.74 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.16), residues: 2771 helix: 1.91 (0.11), residues: 2066 sheet: -1.23 (1.17), residues: 18 loop : -0.98 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP e 74 HIS 0.005 0.001 HIS L 81 PHE 0.037 0.002 PHE a 419 TYR 0.054 0.002 TYR i 144 ARG 0.005 0.000 ARG j 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 751 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 707 time to evaluate : 2.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 21 residues processed: 725 average time/residue: 0.3142 time to fit residues: 363.9670 Evaluate side-chains 677 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 656 time to evaluate : 2.553 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.2048 time to fit residues: 11.3379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 260 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 197 optimal weight: 0.9980 chunk 152 optimal weight: 0.8980 chunk 227 optimal weight: 0.7980 chunk 150 optimal weight: 3.9990 chunk 268 optimal weight: 0.8980 chunk 168 optimal weight: 0.0770 chunk 163 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 HIS ** L 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 96 HIS ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21414 Z= 0.224 Angle : 0.706 13.846 29025 Z= 0.361 Chirality : 0.043 0.321 3434 Planarity : 0.004 0.048 3606 Dihedral : 4.100 18.706 2978 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.49 % Allowed : 28.70 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.16), residues: 2771 helix: 1.90 (0.11), residues: 2087 sheet: -1.11 (1.19), residues: 18 loop : -1.08 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP e 74 HIS 0.004 0.001 HIS L 81 PHE 0.034 0.002 PHE h 90 TYR 0.061 0.002 TYR i 144 ARG 0.008 0.001 ARG j 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 706 time to evaluate : 2.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 18 residues processed: 719 average time/residue: 0.2980 time to fit residues: 343.1900 Evaluate side-chains 681 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 663 time to evaluate : 2.427 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2060 time to fit residues: 9.9881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 166 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 160 optimal weight: 0.8980 chunk 81 optimal weight: 0.5980 chunk 52 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 211 optimal weight: 1.9990 chunk 244 optimal weight: 0.0060 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 HIS ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 338 GLN p 330 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21414 Z= 0.224 Angle : 0.724 12.364 29025 Z= 0.368 Chirality : 0.043 0.312 3434 Planarity : 0.005 0.053 3606 Dihedral : 4.109 19.709 2978 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.59 % Allowed : 30.10 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.16), residues: 2771 helix: 1.87 (0.11), residues: 2083 sheet: -1.30 (1.13), residues: 18 loop : -1.09 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP e 74 HIS 0.004 0.001 HIS L 33 PHE 0.035 0.002 PHE j 108 TYR 0.063 0.002 TYR i 144 ARG 0.006 0.001 ARG d 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 694 time to evaluate : 2.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 22 residues processed: 709 average time/residue: 0.3099 time to fit residues: 351.2612 Evaluate side-chains 666 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 644 time to evaluate : 2.528 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2087 time to fit residues: 11.8374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 257 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 chunk 250 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 196 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 226 optimal weight: 0.8980 chunk 237 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 33 HIS L 82 GLN ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 812 GLN ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 92 GLN ** m 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 6 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21414 Z= 0.275 Angle : 0.776 13.396 29025 Z= 0.392 Chirality : 0.045 0.305 3434 Planarity : 0.005 0.052 3606 Dihedral : 4.157 21.972 2978 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.89 % Allowed : 31.78 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.16), residues: 2771 helix: 1.79 (0.11), residues: 2090 sheet: -1.50 (1.11), residues: 18 loop : -1.09 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP e 74 HIS 0.005 0.001 HIS L 81 PHE 0.035 0.002 PHE L 52 TYR 0.063 0.002 TYR i 144 ARG 0.006 0.001 ARG H 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 693 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 700 average time/residue: 0.3041 time to fit residues: 339.8914 Evaluate side-chains 661 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 651 time to evaluate : 2.445 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1957 time to fit residues: 6.8745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 264 optimal weight: 0.8980 chunk 161 optimal weight: 0.3980 chunk 125 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 277 optimal weight: 0.9990 chunk 255 optimal weight: 4.9990 chunk 221 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 175 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21414 Z= 0.261 Angle : 0.789 12.266 29025 Z= 0.396 Chirality : 0.045 0.317 3434 Planarity : 0.005 0.054 3606 Dihedral : 4.186 25.733 2978 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.65 % Allowed : 33.13 % Favored : 66.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.16), residues: 2771 helix: 1.74 (0.11), residues: 2068 sheet: -1.45 (1.14), residues: 18 loop : -1.02 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP e 74 HIS 0.004 0.001 HIS a 412 PHE 0.042 0.002 PHE j 13 TYR 0.047 0.002 TYR l 68 ARG 0.007 0.001 ARG H 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5542 Ramachandran restraints generated. 2771 Oldfield, 0 Emsley, 2771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 686 time to evaluate : 2.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 693 average time/residue: 0.3078 time to fit residues: 338.0242 Evaluate side-chains 662 residues out of total 2225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 656 time to evaluate : 2.400 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1982 time to fit residues: 5.2980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 235 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 221 optimal weight: 10.0000 chunk 92 optimal weight: 0.9990 chunk 227 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 194 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 48 HIS ** d 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 59 GLN e 61 ASN ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 92 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.106781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.093724 restraints weight = 50953.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.096636 restraints weight = 23959.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.098483 restraints weight = 13715.970| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.6390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21414 Z= 0.249 Angle : 0.795 14.684 29025 Z= 0.400 Chirality : 0.045 0.367 3434 Planarity : 0.005 0.054 3606 Dihedral : 4.207 26.791 2978 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.56 % Allowed : 33.69 % Favored : 65.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.16), residues: 2771 helix: 1.71 (0.11), residues: 2081 sheet: -1.08 (0.87), residues: 33 loop : -1.07 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP e 74 HIS 0.005 0.001 HIS d 88 PHE 0.042 0.002 PHE j 13 TYR 0.048 0.002 TYR l 68 ARG 0.007 0.001 ARG H 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6242.36 seconds wall clock time: 112 minutes 29.03 seconds (6749.03 seconds total)