Starting phenix.real_space_refine on Thu Mar 14 19:18:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk0_21222/03_2024/6vk0_21222.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk0_21222/03_2024/6vk0_21222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk0_21222/03_2024/6vk0_21222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk0_21222/03_2024/6vk0_21222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk0_21222/03_2024/6vk0_21222.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk0_21222/03_2024/6vk0_21222.pdb" } resolution = 4.1 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= 0.008 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 44 5.16 5 C 6267 2.51 5 N 1561 2.21 5 O 1687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 560": "OE1" <-> "OE2" Residue "D ARG 753": "NH1" <-> "NH2" Residue "C PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 124": "OE1" <-> "OE2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "A GLU 70": "OE1" <-> "OE2" Residue "A GLU 104": "OE1" <-> "OE2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 248": "OE1" <-> "OE2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A GLU 503": "OE1" <-> "OE2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "B GLU 78": "OE1" <-> "OE2" Residue "B GLU 213": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9559 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 823 Classifications: {'peptide': 97} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 89} Chain breaks: 1 Chain: "C" Number of atoms: 1470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1470 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 5, 'TRANS': 174} Chain: "A" Number of atoms: 4923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 603, 4923 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 20, 'TRANS': 582} Chain breaks: 4 Chain: "B" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2343 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 5.51, per 1000 atoms: 0.58 Number of scatterers: 9559 At special positions: 0 Unit cell: (110.7, 99.9, 148.5, 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 44 16.00 O 1687 8.00 N 1561 7.00 C 6267 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: 3.74 Conformation dependent library (CDL) restraints added in 1.5 seconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2230 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 79.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'D' and resid 535 through 544 removed outlier: 3.800A pdb=" N VAL D 539 " --> pdb=" O PRO D 535 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU D 540 " --> pdb=" O LEU D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 549 through 551 No H-bonds generated for 'chain 'D' and resid 549 through 551' Processing helix chain 'D' and resid 552 through 562 removed outlier: 4.358A pdb=" N PHE D 556 " --> pdb=" O LEU D 552 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE D 557 " --> pdb=" O VAL D 553 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE D 558 " --> pdb=" O PRO D 554 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 565 No H-bonds generated for 'chain 'D' and resid 563 through 565' Processing helix chain 'D' and resid 566 through 567 No H-bonds generated for 'chain 'D' and resid 566 through 567' Processing helix chain 'D' and resid 568 through 581 removed outlier: 3.853A pdb=" N THR D 581 " --> pdb=" O PHE D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 746 through 753 Processing helix chain 'D' and resid 763 through 778 removed outlier: 3.522A pdb=" N VAL D 777 " --> pdb=" O VAL D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 780 through 789 removed outlier: 4.103A pdb=" N LYS D 786 " --> pdb=" O TYR D 782 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 32 Processing helix chain 'C' and resid 43 through 51 removed outlier: 3.537A pdb=" N VAL C 47 " --> pdb=" O SER C 43 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS C 49 " --> pdb=" O ASP C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 58 removed outlier: 3.806A pdb=" N LEU C 57 " --> pdb=" O TYR C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 61 No H-bonds generated for 'chain 'C' and resid 59 through 61' Processing helix chain 'C' and resid 67 through 85 Processing helix chain 'C' and resid 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 92 through 110 removed outlier: 3.741A pdb=" N TRP C 96 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N PHE C 99 " --> pdb=" O CYS C 95 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU C 100 " --> pdb=" O TRP C 96 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 105 " --> pdb=" O LEU C 101 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL C 106 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N LYS C 107 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET C 108 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 134 Processing helix chain 'C' and resid 152 through 165 removed outlier: 3.805A pdb=" N TYR C 156 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 176 through 192 removed outlier: 4.126A pdb=" N ILE C 189 " --> pdb=" O MET C 185 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY C 190 " --> pdb=" O ASP C 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 42 through 47 removed outlier: 3.579A pdb=" N GLU A 46 " --> pdb=" O ASP A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 83 through 100 Processing helix chain 'A' and resid 105 through 116 Processing helix chain 'A' and resid 123 through 139 removed outlier: 3.591A pdb=" N HIS A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.608A pdb=" N ILE A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.734A pdb=" N GLY A 185 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 197 Processing helix chain 'A' and resid 206 through 225 removed outlier: 3.785A pdb=" N SER A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.514A pdb=" N ASP A 231 " --> pdb=" O ARG A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 removed outlier: 3.694A pdb=" N ILE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 removed outlier: 4.186A pdb=" N ALA A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 361 removed outlier: 3.576A pdb=" N ASN A 360 " --> pdb=" O HIS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 removed outlier: 3.895A pdb=" N TYR A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 407 removed outlier: 3.867A pdb=" N ARG A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 410 No H-bonds generated for 'chain 'A' and resid 408 through 410' Processing helix chain 'A' and resid 412 through 426 Processing helix chain 'A' and resid 429 through 441 removed outlier: 3.982A pdb=" N ALA A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 462 through 465 removed outlier: 4.005A pdb=" N LYS A 465 " --> pdb=" O PRO A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 468 through 480 Processing helix chain 'A' and resid 481 through 495 removed outlier: 3.699A pdb=" N ILE A 485 " --> pdb=" O PHE A 481 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 495 " --> pdb=" O MET A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 517 removed outlier: 4.228A pdb=" N GLU A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 removed outlier: 3.696A pdb=" N THR A 526 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 550 removed outlier: 3.933A pdb=" N ALA A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLN A 549 " --> pdb=" O GLN A 545 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.590A pdb=" N LYS A 580 " --> pdb=" O THR A 576 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N SER A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 610 removed outlier: 3.842A pdb=" N VAL A 600 " --> pdb=" O ILE A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 624 removed outlier: 4.414A pdb=" N ALA A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 618 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 647 through 662 removed outlier: 3.827A pdb=" N ASP A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 685 removed outlier: 3.724A pdb=" N ILE A 685 " --> pdb=" O TRP A 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 31 Processing helix chain 'B' and resid 34 through 43 removed outlier: 3.729A pdb=" N ASN B 43 " --> pdb=" O THR B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 71 Processing helix chain 'B' and resid 75 through 99 Proline residue: B 87 - end of helix removed outlier: 3.544A pdb=" N LEU B 99 " --> pdb=" O PHE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 104 Processing helix chain 'B' and resid 105 through 135 removed outlier: 4.162A pdb=" N ALA B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 175 Processing helix chain 'B' and resid 179 through 220 removed outlier: 3.658A pdb=" N THR B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 294 removed outlier: 4.252A pdb=" N TYR B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 297 through 324 616 hydrogen bonds defined for protein. 1842 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: 2.60 Time building geometry restraints manager: 4.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2932 1.34 - 1.46: 2414 1.46 - 1.58: 4379 1.58 - 1.70: 0 1.70 - 1.82: 79 Bond restraints: 9804 Sorted by residual: bond pdb=" N LYS D 568 " pdb=" CA LYS D 568 " ideal model delta sigma weight residual 1.457 1.419 0.038 1.35e-02 5.49e+03 8.13e+00 bond pdb=" N SER B 135 " pdb=" CA SER B 135 " ideal model delta sigma weight residual 1.457 1.425 0.032 1.40e-02 5.10e+03 5.19e+00 bond pdb=" CA GLN B 134 " pdb=" C GLN B 134 " ideal model delta sigma weight residual 1.524 1.553 -0.029 1.29e-02 6.01e+03 4.98e+00 bond pdb=" CA SER A 262 " pdb=" CB SER A 262 " ideal model delta sigma weight residual 1.531 1.470 0.061 3.28e-02 9.30e+02 3.46e+00 bond pdb=" CA LEU D 565 " pdb=" C LEU D 565 " ideal model delta sigma weight residual 1.532 1.520 0.012 6.50e-03 2.37e+04 3.42e+00 ... (remaining 9799 not shown) Histogram of bond angle deviations from ideal: 98.45 - 105.62: 163 105.62 - 112.78: 5175 112.78 - 119.95: 3594 119.95 - 127.12: 4246 127.12 - 134.29: 109 Bond angle restraints: 13287 Sorted by residual: angle pdb=" N ASP A 246 " pdb=" CA ASP A 246 " pdb=" C ASP A 246 " ideal model delta sigma weight residual 113.38 102.21 11.17 1.23e+00 6.61e-01 8.25e+01 angle pdb=" N GLY A 253 " pdb=" CA GLY A 253 " pdb=" C GLY A 253 " ideal model delta sigma weight residual 112.48 118.48 -6.00 1.21e+00 6.83e-01 2.46e+01 angle pdb=" N MET C 138 " pdb=" CA MET C 138 " pdb=" C MET C 138 " ideal model delta sigma weight residual 110.68 104.35 6.33 1.39e+00 5.18e-01 2.07e+01 angle pdb=" N THR B 194 " pdb=" CA THR B 194 " pdb=" CB THR B 194 " ideal model delta sigma weight residual 110.07 116.23 -6.16 1.45e+00 4.76e-01 1.80e+01 angle pdb=" C PHE D 564 " pdb=" N LEU D 565 " pdb=" CA LEU D 565 " ideal model delta sigma weight residual 123.10 126.46 -3.36 9.60e-01 1.09e+00 1.22e+01 ... (remaining 13282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 5122 17.87 - 35.74: 525 35.74 - 53.61: 108 53.61 - 71.48: 12 71.48 - 89.35: 5 Dihedral angle restraints: 5772 sinusoidal: 2318 harmonic: 3454 Sorted by residual: dihedral pdb=" CA TRP D 567 " pdb=" C TRP D 567 " pdb=" N LYS D 568 " pdb=" CA LYS D 568 " ideal model delta harmonic sigma weight residual 180.00 155.44 24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA GLU A 104 " pdb=" C GLU A 104 " pdb=" N ALA A 105 " pdb=" CA ALA A 105 " ideal model delta harmonic sigma weight residual 180.00 156.80 23.20 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA VAL C 103 " pdb=" C VAL C 103 " pdb=" N ILE C 104 " pdb=" CA ILE C 104 " ideal model delta harmonic sigma weight residual -180.00 -157.02 -22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 5769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1276 0.068 - 0.137: 186 0.137 - 0.205: 12 0.205 - 0.273: 2 0.273 - 0.341: 2 Chirality restraints: 1478 Sorted by residual: chirality pdb=" CA LEU A 252 " pdb=" N LEU A 252 " pdb=" C LEU A 252 " pdb=" CB LEU A 252 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA SER A 245 " pdb=" N SER A 245 " pdb=" C SER A 245 " pdb=" CB SER A 245 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CB ILE A 37 " pdb=" CA ILE A 37 " pdb=" CG1 ILE A 37 " pdb=" CG2 ILE A 37 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1475 not shown) Planarity restraints: 1642 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 2 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO B 3 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO B 3 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 3 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 244 " -0.011 2.00e-02 2.50e+03 2.05e-02 4.19e+00 pdb=" C ILE A 244 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE A 244 " -0.013 2.00e-02 2.50e+03 pdb=" N SER A 245 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 27 " -0.033 5.00e-02 4.00e+02 4.92e-02 3.88e+00 pdb=" N PRO A 28 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 28 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 28 " -0.028 5.00e-02 4.00e+02 ... (remaining 1639 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1358 2.74 - 3.28: 10666 3.28 - 3.82: 15460 3.82 - 4.36: 17351 4.36 - 4.90: 28036 Nonbonded interactions: 72871 Sorted by model distance: nonbonded pdb=" O ASP D 758 " pdb=" ND2 ASN D 761 " model vdw 2.203 2.520 nonbonded pdb=" NE2 GLN A 424 " pdb=" OE1 GLN A 453 " model vdw 2.209 2.520 nonbonded pdb=" ND2 ASN A 595 " pdb=" OD1 ASP A 597 " model vdw 2.217 2.520 nonbonded pdb=" OG SER A 97 " pdb=" OG1 THR A 106 " model vdw 2.222 2.440 nonbonded pdb=" O GLN A 432 " pdb=" OG SER A 435 " model vdw 2.227 2.440 ... (remaining 72866 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.390 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 27.480 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 9804 Z= 0.446 Angle : 0.844 11.174 13287 Z= 0.493 Chirality : 0.049 0.341 1478 Planarity : 0.005 0.052 1642 Dihedral : 14.838 89.349 3542 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.19 % Allowed : 10.53 % Favored : 89.28 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.49 (0.20), residues: 1140 helix: -1.94 (0.14), residues: 797 sheet: None (None), residues: 0 loop : -2.83 (0.30), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 684 HIS 0.011 0.002 HIS B 286 PHE 0.033 0.002 PHE B 88 TYR 0.029 0.002 TYR B 18 ARG 0.009 0.001 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 320 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 770 LYS cc_start: 0.7796 (mmtt) cc_final: 0.7063 (pttp) REVERT: C 52 GLN cc_start: 0.6224 (tp-100) cc_final: 0.5328 (pm20) REVERT: C 91 ARG cc_start: 0.7374 (mpt180) cc_final: 0.6747 (mtt-85) REVERT: C 99 PHE cc_start: 0.7147 (m-80) cc_final: 0.6472 (m-80) REVERT: C 125 ASN cc_start: 0.8683 (m110) cc_final: 0.8417 (m110) REVERT: C 130 GLU cc_start: 0.8178 (tp30) cc_final: 0.7971 (tp30) REVERT: C 137 GLN cc_start: 0.8181 (mt0) cc_final: 0.7697 (mt0) REVERT: C 166 LYS cc_start: 0.8312 (tppt) cc_final: 0.7994 (tptp) REVERT: C 189 ILE cc_start: 0.5628 (tt) cc_final: 0.5381 (tp) REVERT: C 191 LYS cc_start: 0.8144 (tmtt) cc_final: 0.7708 (tmtt) REVERT: A 49 MET cc_start: 0.8227 (mmm) cc_final: 0.7857 (mmt) REVERT: A 74 TYR cc_start: 0.8360 (t80) cc_final: 0.7932 (t80) REVERT: A 90 TYR cc_start: 0.7917 (t80) cc_final: 0.7485 (t80) REVERT: A 93 LEU cc_start: 0.9416 (mm) cc_final: 0.9082 (mm) REVERT: A 180 ARG cc_start: 0.8196 (tpt170) cc_final: 0.7712 (tpp-160) REVERT: A 256 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8111 (tp) REVERT: A 438 MET cc_start: 0.7660 (mmm) cc_final: 0.6753 (mmm) REVERT: A 439 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7737 (mtpt) REVERT: A 461 PHE cc_start: 0.8370 (m-80) cc_final: 0.7882 (m-80) REVERT: A 520 MET cc_start: 0.8918 (mmm) cc_final: 0.8649 (mmm) REVERT: A 537 GLU cc_start: 0.7733 (tp30) cc_final: 0.7214 (tp30) REVERT: A 614 LYS cc_start: 0.8568 (tttt) cc_final: 0.8083 (mttt) REVERT: B 168 CYS cc_start: 0.8976 (m) cc_final: 0.8264 (t) REVERT: B 186 TYR cc_start: 0.8537 (m-10) cc_final: 0.8265 (m-80) REVERT: B 195 MET cc_start: 0.9083 (mtp) cc_final: 0.8840 (mtm) outliers start: 2 outliers final: 1 residues processed: 322 average time/residue: 0.2308 time to fit residues: 100.9936 Evaluate side-chains 251 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 249 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.0170 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 104 optimal weight: 7.9990 overall best weight: 1.5422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 745 HIS ** D 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 ASN ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN A 86 GLN A 117 GLN A 202 ASN A 429 ASN A 504 ASN A 593 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 286 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9804 Z= 0.211 Angle : 0.658 11.821 13287 Z= 0.346 Chirality : 0.042 0.160 1478 Planarity : 0.005 0.079 1642 Dihedral : 5.457 27.713 1277 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.29 % Allowed : 6.12 % Favored : 93.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.05 (0.24), residues: 1140 helix: -0.06 (0.17), residues: 829 sheet: None (None), residues: 0 loop : -2.23 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 19 HIS 0.013 0.001 HIS B 79 PHE 0.037 0.002 PHE D 534 TYR 0.021 0.002 TYR D 754 ARG 0.014 0.001 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 334 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 770 LYS cc_start: 0.7462 (mmtt) cc_final: 0.6352 (pttp) REVERT: C 39 LYS cc_start: 0.5792 (mttt) cc_final: 0.5215 (mmtt) REVERT: C 75 PHE cc_start: 0.7663 (m-80) cc_final: 0.6729 (m-80) REVERT: C 91 ARG cc_start: 0.7177 (mpt180) cc_final: 0.6685 (mtt180) REVERT: C 99 PHE cc_start: 0.6386 (m-80) cc_final: 0.5723 (m-80) REVERT: C 112 GLU cc_start: 0.6902 (pm20) cc_final: 0.5124 (tm-30) REVERT: C 137 GLN cc_start: 0.8216 (mt0) cc_final: 0.7877 (mt0) REVERT: A 79 GLN cc_start: 0.7979 (mm110) cc_final: 0.7725 (mm110) REVERT: A 93 LEU cc_start: 0.9536 (mm) cc_final: 0.9320 (mm) REVERT: A 132 GLU cc_start: 0.7647 (tp30) cc_final: 0.7335 (tp30) REVERT: A 372 CYS cc_start: 0.9068 (m) cc_final: 0.8668 (m) REVERT: A 438 MET cc_start: 0.7852 (mmm) cc_final: 0.7298 (mmt) REVERT: A 461 PHE cc_start: 0.8124 (m-80) cc_final: 0.7794 (m-10) REVERT: A 478 LEU cc_start: 0.9302 (mt) cc_final: 0.9092 (mt) REVERT: A 520 MET cc_start: 0.8828 (mmm) cc_final: 0.8467 (mmm) REVERT: A 571 ASP cc_start: 0.8582 (t0) cc_final: 0.8362 (t0) REVERT: A 614 LYS cc_start: 0.8545 (tttt) cc_final: 0.7970 (mttt) REVERT: A 639 GLU cc_start: 0.8758 (pp20) cc_final: 0.8097 (pp20) REVERT: A 642 LEU cc_start: 0.7927 (pp) cc_final: 0.6609 (pp) REVERT: A 666 TYR cc_start: 0.7984 (t80) cc_final: 0.7719 (t80) REVERT: A 676 LEU cc_start: 0.7774 (tp) cc_final: 0.7442 (tp) REVERT: A 679 LYS cc_start: 0.8470 (mttt) cc_final: 0.8240 (mtpp) REVERT: B 4 GLU cc_start: 0.6958 (pm20) cc_final: 0.6380 (tm-30) REVERT: B 36 LEU cc_start: 0.8825 (tp) cc_final: 0.8227 (mm) REVERT: B 81 HIS cc_start: 0.8855 (m-70) cc_final: 0.8108 (m-70) REVERT: B 142 MET cc_start: 0.6773 (tpp) cc_final: 0.6498 (tpp) REVERT: B 187 LEU cc_start: 0.8881 (mt) cc_final: 0.8654 (mt) REVERT: B 195 MET cc_start: 0.8906 (mtp) cc_final: 0.8696 (mtm) REVERT: B 289 MET cc_start: 0.6134 (ttt) cc_final: 0.5245 (mmt) REVERT: B 297 MET cc_start: 0.5213 (mtt) cc_final: 0.4977 (mtt) outliers start: 3 outliers final: 1 residues processed: 335 average time/residue: 0.1949 time to fit residues: 93.8800 Evaluate side-chains 258 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 104 optimal weight: 0.9990 chunk 113 optimal weight: 10.0000 chunk 93 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN A 123 ASN A 135 ASN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN B 189 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9804 Z= 0.210 Angle : 0.632 10.711 13287 Z= 0.329 Chirality : 0.041 0.206 1478 Planarity : 0.004 0.062 1642 Dihedral : 5.220 28.719 1277 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.19 % Allowed : 3.64 % Favored : 96.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.18 (0.25), residues: 1140 helix: 0.59 (0.18), residues: 839 sheet: None (None), residues: 0 loop : -2.06 (0.35), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 27 HIS 0.005 0.001 HIS B 79 PHE 0.033 0.002 PHE C 75 TYR 0.017 0.002 TYR A 477 ARG 0.006 0.000 ARG D 542 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 332 time to evaluate : 1.074 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: D 770 LYS cc_start: 0.7965 (mmtt) cc_final: 0.7217 (pttp) REVERT: C 39 LYS cc_start: 0.6197 (mtpt) cc_final: 0.5927 (mmtt) REVERT: C 71 MET cc_start: 0.8141 (tpt) cc_final: 0.7534 (tpt) REVERT: C 72 ILE cc_start: 0.8868 (mt) cc_final: 0.8652 (mt) REVERT: C 75 PHE cc_start: 0.7739 (m-80) cc_final: 0.7062 (m-80) REVERT: C 99 PHE cc_start: 0.6416 (m-80) cc_final: 0.5863 (m-80) REVERT: C 109 THR cc_start: 0.7563 (t) cc_final: 0.6704 (t) REVERT: C 112 GLU cc_start: 0.7696 (pm20) cc_final: 0.5101 (tm-30) REVERT: C 120 VAL cc_start: 0.8146 (t) cc_final: 0.6602 (t) REVERT: C 121 LEU cc_start: 0.9236 (mt) cc_final: 0.8929 (mt) REVERT: C 137 GLN cc_start: 0.8078 (mt0) cc_final: 0.7819 (mt0) REVERT: A 79 GLN cc_start: 0.8052 (mm110) cc_final: 0.7711 (mm110) REVERT: A 93 LEU cc_start: 0.9501 (mm) cc_final: 0.9193 (mm) REVERT: A 124 MET cc_start: 0.8536 (tpp) cc_final: 0.8336 (tpp) REVERT: A 372 CYS cc_start: 0.9057 (m) cc_final: 0.8656 (m) REVERT: A 491 MET cc_start: 0.7998 (mmp) cc_final: 0.7772 (ttt) REVERT: A 520 MET cc_start: 0.8795 (mmm) cc_final: 0.8502 (mmm) REVERT: A 534 ASP cc_start: 0.8553 (t70) cc_final: 0.8220 (t70) REVERT: A 571 ASP cc_start: 0.8642 (t0) cc_final: 0.8345 (t0) REVERT: A 614 LYS cc_start: 0.8488 (tttt) cc_final: 0.7932 (mttt) REVERT: B 1 MET cc_start: 0.2309 (mmt) cc_final: 0.1908 (mmt) REVERT: B 4 GLU cc_start: 0.6975 (pm20) cc_final: 0.6305 (tm-30) REVERT: B 36 LEU cc_start: 0.8934 (tp) cc_final: 0.8347 (mm) REVERT: B 81 HIS cc_start: 0.8827 (m-70) cc_final: 0.8053 (m-70) REVERT: B 95 PHE cc_start: 0.7704 (t80) cc_final: 0.7289 (t80) REVERT: B 142 MET cc_start: 0.6678 (tpp) cc_final: 0.6374 (tpp) REVERT: B 192 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8528 (mm-30) outliers start: 2 outliers final: 0 residues processed: 332 average time/residue: 0.1710 time to fit residues: 83.1037 Evaluate side-chains 266 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 10.0000 chunk 78 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 49 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN A 88 HIS A 113 HIS A 123 ASN A 564 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 640 HIS B 79 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7672 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9804 Z= 0.234 Angle : 0.636 10.677 13287 Z= 0.327 Chirality : 0.041 0.166 1478 Planarity : 0.004 0.063 1642 Dihedral : 5.130 27.161 1277 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.14 (0.25), residues: 1140 helix: 0.84 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -1.95 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 27 HIS 0.010 0.001 HIS B 79 PHE 0.020 0.002 PHE D 544 TYR 0.019 0.001 TYR A 90 ARG 0.004 0.000 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 1.047 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: D 770 LYS cc_start: 0.7995 (mmtt) cc_final: 0.7186 (pttp) REVERT: C 39 LYS cc_start: 0.6217 (mtpt) cc_final: 0.5923 (mmtt) REVERT: C 71 MET cc_start: 0.8080 (tpt) cc_final: 0.7467 (tpt) REVERT: C 75 PHE cc_start: 0.7777 (m-80) cc_final: 0.7287 (m-80) REVERT: C 99 PHE cc_start: 0.6304 (m-80) cc_final: 0.5774 (m-80) REVERT: C 120 VAL cc_start: 0.8324 (t) cc_final: 0.6851 (t) REVERT: C 121 LEU cc_start: 0.9339 (mt) cc_final: 0.9101 (mt) REVERT: C 125 ASN cc_start: 0.8864 (m-40) cc_final: 0.8585 (m110) REVERT: C 137 GLN cc_start: 0.7889 (mt0) cc_final: 0.7630 (tt0) REVERT: A 79 GLN cc_start: 0.8135 (mm110) cc_final: 0.7819 (mm110) REVERT: A 93 LEU cc_start: 0.9491 (mm) cc_final: 0.9155 (mm) REVERT: A 132 GLU cc_start: 0.8013 (tp30) cc_final: 0.7635 (tp30) REVERT: A 246 ASP cc_start: 0.8911 (m-30) cc_final: 0.8380 (m-30) REVERT: A 372 CYS cc_start: 0.9054 (m) cc_final: 0.8708 (m) REVERT: A 438 MET cc_start: 0.7968 (mmt) cc_final: 0.7352 (mmm) REVERT: A 534 ASP cc_start: 0.8569 (t70) cc_final: 0.8217 (t70) REVERT: A 571 ASP cc_start: 0.8515 (t0) cc_final: 0.8152 (t0) REVERT: A 614 LYS cc_start: 0.8453 (tttt) cc_final: 0.7828 (mttt) REVERT: A 628 ILE cc_start: 0.8883 (mt) cc_final: 0.8679 (mm) REVERT: B 4 GLU cc_start: 0.7044 (pm20) cc_final: 0.6463 (tm-30) REVERT: B 32 SER cc_start: 0.8175 (t) cc_final: 0.7474 (t) REVERT: B 36 LEU cc_start: 0.8856 (tp) cc_final: 0.8208 (mm) REVERT: B 37 GLN cc_start: 0.8772 (tt0) cc_final: 0.8062 (tt0) REVERT: B 81 HIS cc_start: 0.8817 (m-70) cc_final: 0.8030 (m-70) REVERT: B 95 PHE cc_start: 0.7675 (t80) cc_final: 0.7444 (t80) REVERT: B 142 MET cc_start: 0.6701 (tpp) cc_final: 0.6374 (tpp) REVERT: B 204 PHE cc_start: 0.8124 (t80) cc_final: 0.7744 (t80) REVERT: B 289 MET cc_start: 0.5517 (ttt) cc_final: 0.5303 (mmt) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.1715 time to fit residues: 81.0141 Evaluate side-chains 269 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 63 optimal weight: 6.9990 chunk 1 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 76 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 28 optimal weight: 0.0670 chunk 37 optimal weight: 5.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 HIS A 479 ASN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9804 Z= 0.268 Angle : 0.649 10.121 13287 Z= 0.339 Chirality : 0.042 0.217 1478 Planarity : 0.004 0.059 1642 Dihedral : 5.148 27.764 1277 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.16 (0.25), residues: 1140 helix: 0.86 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -1.93 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 27 HIS 0.004 0.001 HIS B 79 PHE 0.020 0.002 PHE D 544 TYR 0.020 0.002 TYR A 90 ARG 0.012 0.000 ARG C 141 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 1.065 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: D 770 LYS cc_start: 0.8053 (mmtt) cc_final: 0.7206 (pttp) REVERT: C 39 LYS cc_start: 0.6341 (mtpt) cc_final: 0.6023 (mmtt) REVERT: C 71 MET cc_start: 0.8002 (tpt) cc_final: 0.6965 (tpp) REVERT: C 75 PHE cc_start: 0.7740 (m-80) cc_final: 0.6588 (m-80) REVERT: C 99 PHE cc_start: 0.6239 (m-80) cc_final: 0.5722 (m-80) REVERT: C 120 VAL cc_start: 0.8257 (t) cc_final: 0.6793 (t) REVERT: C 121 LEU cc_start: 0.9323 (mt) cc_final: 0.9074 (mt) REVERT: C 125 ASN cc_start: 0.8738 (m-40) cc_final: 0.8482 (m-40) REVERT: C 137 GLN cc_start: 0.7952 (mt0) cc_final: 0.7621 (tt0) REVERT: C 177 MET cc_start: 0.8157 (tpp) cc_final: 0.7778 (mmm) REVERT: A 93 LEU cc_start: 0.9428 (mm) cc_final: 0.9164 (mm) REVERT: A 132 GLU cc_start: 0.7914 (tp30) cc_final: 0.7538 (tp30) REVERT: A 232 ILE cc_start: 0.8571 (mm) cc_final: 0.8100 (mp) REVERT: A 246 ASP cc_start: 0.8884 (m-30) cc_final: 0.8346 (m-30) REVERT: A 372 CYS cc_start: 0.9069 (m) cc_final: 0.8720 (m) REVERT: A 434 ILE cc_start: 0.9424 (mp) cc_final: 0.9081 (mp) REVERT: A 438 MET cc_start: 0.7976 (mmt) cc_final: 0.7758 (mmm) REVERT: A 520 MET cc_start: 0.8648 (mmm) cc_final: 0.8382 (mmm) REVERT: A 534 ASP cc_start: 0.8572 (t70) cc_final: 0.8231 (t70) REVERT: A 571 ASP cc_start: 0.8558 (t0) cc_final: 0.8241 (t0) REVERT: A 614 LYS cc_start: 0.8398 (tttt) cc_final: 0.7833 (mttp) REVERT: B 4 GLU cc_start: 0.7137 (pm20) cc_final: 0.6561 (tm-30) REVERT: B 36 LEU cc_start: 0.8858 (tp) cc_final: 0.8239 (mm) REVERT: B 81 HIS cc_start: 0.8878 (m-70) cc_final: 0.8101 (m-70) REVERT: B 95 PHE cc_start: 0.7686 (t80) cc_final: 0.7278 (t80) REVERT: B 142 MET cc_start: 0.6599 (tpp) cc_final: 0.6337 (tpp) REVERT: B 204 PHE cc_start: 0.8085 (t80) cc_final: 0.7745 (t80) REVERT: B 289 MET cc_start: 0.5327 (ttt) cc_final: 0.5075 (mmt) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.1761 time to fit residues: 80.6051 Evaluate side-chains 261 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 100 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS B 312 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9804 Z= 0.209 Angle : 0.635 10.556 13287 Z= 0.331 Chirality : 0.042 0.182 1478 Planarity : 0.004 0.054 1642 Dihedral : 5.083 27.225 1277 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.26 (0.25), residues: 1140 helix: 0.94 (0.18), residues: 843 sheet: None (None), residues: 0 loop : -2.02 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 27 HIS 0.023 0.002 HIS C 180 PHE 0.049 0.002 PHE C 88 TYR 0.018 0.001 TYR A 636 ARG 0.003 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 1.025 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: D 770 LYS cc_start: 0.8001 (mmtt) cc_final: 0.7151 (pttp) REVERT: C 39 LYS cc_start: 0.6329 (mtpt) cc_final: 0.6023 (mmtt) REVERT: C 71 MET cc_start: 0.7911 (tpt) cc_final: 0.7412 (tpt) REVERT: C 75 PHE cc_start: 0.7537 (m-80) cc_final: 0.7099 (m-80) REVERT: C 94 PHE cc_start: 0.5618 (p90) cc_final: 0.5345 (p90) REVERT: C 99 PHE cc_start: 0.6132 (m-80) cc_final: 0.5606 (m-80) REVERT: C 120 VAL cc_start: 0.8324 (t) cc_final: 0.6913 (t) REVERT: C 121 LEU cc_start: 0.9361 (mt) cc_final: 0.8992 (mt) REVERT: C 137 GLN cc_start: 0.8059 (mt0) cc_final: 0.7836 (mt0) REVERT: A 93 LEU cc_start: 0.9428 (mm) cc_final: 0.9118 (mm) REVERT: A 132 GLU cc_start: 0.7957 (tp30) cc_final: 0.7529 (tp30) REVERT: A 138 THR cc_start: 0.8187 (m) cc_final: 0.7975 (t) REVERT: A 246 ASP cc_start: 0.8795 (m-30) cc_final: 0.8298 (m-30) REVERT: A 372 CYS cc_start: 0.9044 (m) cc_final: 0.8691 (m) REVERT: A 438 MET cc_start: 0.7973 (mmt) cc_final: 0.7465 (mmm) REVERT: A 441 MET cc_start: 0.8244 (mtt) cc_final: 0.8031 (mtt) REVERT: A 520 MET cc_start: 0.8669 (mmm) cc_final: 0.8191 (mmm) REVERT: A 534 ASP cc_start: 0.8557 (t70) cc_final: 0.8235 (t70) REVERT: A 571 ASP cc_start: 0.8588 (t0) cc_final: 0.8210 (t0) REVERT: A 614 LYS cc_start: 0.8359 (tttt) cc_final: 0.7721 (mttp) REVERT: A 652 LYS cc_start: 0.8371 (tttt) cc_final: 0.8144 (mttm) REVERT: B 4 GLU cc_start: 0.7125 (pm20) cc_final: 0.6606 (tm-30) REVERT: B 36 LEU cc_start: 0.8890 (tp) cc_final: 0.8434 (mm) REVERT: B 81 HIS cc_start: 0.8854 (m-70) cc_final: 0.8066 (m-70) REVERT: B 85 ARG cc_start: 0.7000 (mtt-85) cc_final: 0.6578 (tpt170) REVERT: B 142 MET cc_start: 0.6833 (tpp) cc_final: 0.6523 (tpp) REVERT: B 204 PHE cc_start: 0.7989 (t80) cc_final: 0.7649 (t80) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.1804 time to fit residues: 80.9287 Evaluate side-chains 267 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 12 optimal weight: 9.9990 chunk 63 optimal weight: 10.0000 chunk 81 optimal weight: 0.0470 chunk 62 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 110 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS A 117 GLN A 123 ASN A 564 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9804 Z= 0.294 Angle : 0.679 9.760 13287 Z= 0.354 Chirality : 0.043 0.181 1478 Planarity : 0.004 0.053 1642 Dihedral : 5.120 29.234 1277 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.21 (0.25), residues: 1140 helix: 0.91 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -1.98 (0.36), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 27 HIS 0.024 0.002 HIS C 180 PHE 0.033 0.002 PHE D 775 TYR 0.024 0.002 TYR C 165 ARG 0.005 0.000 ARG C 91 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.034 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: D 770 LYS cc_start: 0.7967 (mmtt) cc_final: 0.7160 (pttp) REVERT: C 71 MET cc_start: 0.7941 (tpt) cc_final: 0.7549 (tpt) REVERT: C 75 PHE cc_start: 0.7723 (m-80) cc_final: 0.7304 (m-80) REVERT: C 91 ARG cc_start: 0.7172 (mtt180) cc_final: 0.6730 (mtt180) REVERT: C 99 PHE cc_start: 0.6092 (m-80) cc_final: 0.5577 (m-80) REVERT: C 120 VAL cc_start: 0.8448 (t) cc_final: 0.7021 (t) REVERT: C 121 LEU cc_start: 0.9405 (mt) cc_final: 0.9150 (mt) REVERT: C 191 LYS cc_start: 0.7664 (tmtt) cc_final: 0.7208 (tmtt) REVERT: A 74 TYR cc_start: 0.7520 (t80) cc_final: 0.7236 (t80) REVERT: A 93 LEU cc_start: 0.9437 (mm) cc_final: 0.9128 (mm) REVERT: A 132 GLU cc_start: 0.7988 (tp30) cc_final: 0.7524 (tp30) REVERT: A 372 CYS cc_start: 0.9056 (m) cc_final: 0.8694 (m) REVERT: A 438 MET cc_start: 0.7976 (mmt) cc_final: 0.7476 (mmm) REVERT: A 441 MET cc_start: 0.8183 (mtt) cc_final: 0.7944 (mtt) REVERT: A 520 MET cc_start: 0.8673 (mmm) cc_final: 0.8302 (mmm) REVERT: A 534 ASP cc_start: 0.8560 (t70) cc_final: 0.8250 (t70) REVERT: A 571 ASP cc_start: 0.8526 (t0) cc_final: 0.8172 (t0) REVERT: A 614 LYS cc_start: 0.8437 (tttt) cc_final: 0.7882 (mttp) REVERT: A 652 LYS cc_start: 0.8426 (tttt) cc_final: 0.8206 (mttm) REVERT: A 666 TYR cc_start: 0.7385 (t80) cc_final: 0.7179 (t80) REVERT: B 4 GLU cc_start: 0.7261 (pm20) cc_final: 0.6702 (tm-30) REVERT: B 36 LEU cc_start: 0.8929 (tp) cc_final: 0.8423 (mm) REVERT: B 81 HIS cc_start: 0.8905 (m-70) cc_final: 0.8050 (m-70) REVERT: B 168 CYS cc_start: 0.8999 (m) cc_final: 0.8789 (m) REVERT: B 204 PHE cc_start: 0.7996 (t80) cc_final: 0.7676 (t80) REVERT: B 289 MET cc_start: 0.3794 (mmt) cc_final: 0.3481 (mmt) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1761 time to fit residues: 75.7293 Evaluate side-chains 254 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 21 optimal weight: 0.0570 chunk 70 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 771 ASN A 123 ASN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 640 HIS B 312 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9804 Z= 0.190 Angle : 0.636 10.795 13287 Z= 0.327 Chirality : 0.041 0.191 1478 Planarity : 0.004 0.051 1642 Dihedral : 4.924 27.081 1277 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.38 (0.25), residues: 1140 helix: 1.10 (0.18), residues: 835 sheet: None (None), residues: 0 loop : -2.14 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 27 HIS 0.013 0.001 HIS C 180 PHE 0.023 0.002 PHE D 775 TYR 0.016 0.001 TYR A 636 ARG 0.008 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.046 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: D 770 LYS cc_start: 0.7959 (mmtt) cc_final: 0.6919 (ttpp) REVERT: C 71 MET cc_start: 0.7886 (tpt) cc_final: 0.7502 (tpt) REVERT: C 75 PHE cc_start: 0.7576 (m-80) cc_final: 0.7109 (m-80) REVERT: C 91 ARG cc_start: 0.7120 (mtt180) cc_final: 0.6790 (mtt180) REVERT: C 99 PHE cc_start: 0.5897 (m-80) cc_final: 0.5457 (m-80) REVERT: C 120 VAL cc_start: 0.8225 (t) cc_final: 0.6807 (t) REVERT: C 121 LEU cc_start: 0.9371 (mt) cc_final: 0.8982 (mt) REVERT: C 177 MET cc_start: 0.8146 (tpp) cc_final: 0.7615 (mmm) REVERT: C 184 TYR cc_start: 0.6837 (t80) cc_final: 0.6130 (t80) REVERT: A 74 TYR cc_start: 0.7367 (t80) cc_final: 0.7054 (t80) REVERT: A 372 CYS cc_start: 0.9023 (m) cc_final: 0.8648 (m) REVERT: A 374 GLN cc_start: 0.8511 (mt0) cc_final: 0.8013 (mm-40) REVERT: A 473 MET cc_start: 0.8865 (mmm) cc_final: 0.8658 (mmt) REVERT: A 499 LYS cc_start: 0.8057 (mmtp) cc_final: 0.7231 (tptm) REVERT: A 520 MET cc_start: 0.8589 (mmm) cc_final: 0.8164 (mmm) REVERT: A 534 ASP cc_start: 0.8530 (t70) cc_final: 0.8144 (t0) REVERT: A 570 GLU cc_start: 0.7956 (tp30) cc_final: 0.7755 (tp30) REVERT: A 571 ASP cc_start: 0.8606 (t0) cc_final: 0.8331 (t0) REVERT: A 614 LYS cc_start: 0.8200 (tttt) cc_final: 0.7721 (mttp) REVERT: A 652 LYS cc_start: 0.8397 (tttt) cc_final: 0.8140 (mttm) REVERT: B 4 GLU cc_start: 0.7051 (pm20) cc_final: 0.6560 (tm-30) REVERT: B 36 LEU cc_start: 0.8957 (tp) cc_final: 0.8507 (mm) REVERT: B 81 HIS cc_start: 0.8926 (m-70) cc_final: 0.8029 (m90) REVERT: B 168 CYS cc_start: 0.9008 (m) cc_final: 0.8759 (m) REVERT: B 188 ILE cc_start: 0.9306 (tt) cc_final: 0.8881 (tt) REVERT: B 204 PHE cc_start: 0.7973 (t80) cc_final: 0.7663 (t80) REVERT: B 289 MET cc_start: 0.3828 (mmt) cc_final: 0.3450 (mmt) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1777 time to fit residues: 80.1007 Evaluate side-chains 255 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 255 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 81 optimal weight: 0.0270 chunk 31 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 97 optimal weight: 20.0000 chunk 102 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 overall best weight: 1.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 79 HIS B 312 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9804 Z= 0.202 Angle : 0.656 11.982 13287 Z= 0.334 Chirality : 0.042 0.174 1478 Planarity : 0.004 0.050 1642 Dihedral : 4.854 26.922 1277 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.41 (0.25), residues: 1140 helix: 1.12 (0.18), residues: 839 sheet: None (None), residues: 0 loop : -2.15 (0.36), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 169 HIS 0.010 0.001 HIS C 180 PHE 0.024 0.002 PHE C 88 TYR 0.022 0.001 TYR C 165 ARG 0.002 0.000 ARG C 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 568 LYS cc_start: 0.7247 (tptm) cc_final: 0.6751 (tptp) REVERT: D 770 LYS cc_start: 0.7898 (mmtt) cc_final: 0.7031 (pttp) REVERT: C 71 MET cc_start: 0.7894 (tpt) cc_final: 0.7497 (tpt) REVERT: C 75 PHE cc_start: 0.7633 (m-80) cc_final: 0.7171 (m-80) REVERT: C 91 ARG cc_start: 0.7128 (mtt180) cc_final: 0.6836 (mtt180) REVERT: C 99 PHE cc_start: 0.5826 (m-80) cc_final: 0.5425 (m-80) REVERT: C 120 VAL cc_start: 0.8333 (t) cc_final: 0.7004 (t) REVERT: C 121 LEU cc_start: 0.9409 (mt) cc_final: 0.9114 (mt) REVERT: C 177 MET cc_start: 0.8097 (tpp) cc_final: 0.7579 (mmm) REVERT: C 191 LYS cc_start: 0.7642 (tmtt) cc_final: 0.7198 (tmtt) REVERT: A 74 TYR cc_start: 0.7310 (t80) cc_final: 0.7079 (t80) REVERT: A 372 CYS cc_start: 0.9009 (m) cc_final: 0.8652 (m) REVERT: A 374 GLN cc_start: 0.8510 (mt0) cc_final: 0.7997 (mm-40) REVERT: A 499 LYS cc_start: 0.8067 (mmtp) cc_final: 0.7242 (tptm) REVERT: A 520 MET cc_start: 0.8603 (mmm) cc_final: 0.8158 (mmm) REVERT: A 534 ASP cc_start: 0.8553 (t70) cc_final: 0.8173 (t0) REVERT: A 571 ASP cc_start: 0.8602 (t0) cc_final: 0.8338 (t0) REVERT: A 614 LYS cc_start: 0.8230 (tttt) cc_final: 0.7887 (mttp) REVERT: A 652 LYS cc_start: 0.8380 (tttt) cc_final: 0.8151 (mttm) REVERT: A 666 TYR cc_start: 0.7361 (t80) cc_final: 0.7074 (t80) REVERT: B 36 LEU cc_start: 0.8911 (tp) cc_final: 0.8497 (mm) REVERT: B 81 HIS cc_start: 0.8913 (m-70) cc_final: 0.8046 (m-70) REVERT: B 168 CYS cc_start: 0.8997 (m) cc_final: 0.8771 (m) REVERT: B 204 PHE cc_start: 0.8018 (t80) cc_final: 0.7722 (t80) REVERT: B 289 MET cc_start: 0.3815 (mmt) cc_final: 0.3339 (mmm) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1790 time to fit residues: 80.0866 Evaluate side-chains 260 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 66 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 9 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 ASN ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9804 Z= 0.166 Angle : 0.647 12.193 13287 Z= 0.325 Chirality : 0.041 0.181 1478 Planarity : 0.004 0.048 1642 Dihedral : 4.726 23.467 1277 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.50 (0.25), residues: 1140 helix: 1.18 (0.18), residues: 847 sheet: None (None), residues: 0 loop : -2.20 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP C 96 HIS 0.011 0.001 HIS C 180 PHE 0.026 0.001 PHE C 88 TYR 0.018 0.001 TYR A 380 ARG 0.004 0.000 ARG A 407 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 568 LYS cc_start: 0.7218 (tptm) cc_final: 0.6603 (tptp) REVERT: D 573 LEU cc_start: 0.8301 (tp) cc_final: 0.7987 (tp) REVERT: D 770 LYS cc_start: 0.7817 (mmtt) cc_final: 0.6740 (ttpp) REVERT: C 71 MET cc_start: 0.7851 (tpt) cc_final: 0.7474 (tpt) REVERT: C 75 PHE cc_start: 0.7609 (m-80) cc_final: 0.7092 (m-80) REVERT: C 91 ARG cc_start: 0.7082 (mtt180) cc_final: 0.6149 (mtm-85) REVERT: C 99 PHE cc_start: 0.5784 (m-80) cc_final: 0.5398 (m-80) REVERT: C 120 VAL cc_start: 0.8304 (t) cc_final: 0.6974 (t) REVERT: C 121 LEU cc_start: 0.9422 (mt) cc_final: 0.9104 (mt) REVERT: C 138 MET cc_start: 0.6756 (tpt) cc_final: 0.6366 (tpt) REVERT: C 177 MET cc_start: 0.8116 (tpp) cc_final: 0.7542 (mmm) REVERT: C 184 TYR cc_start: 0.7428 (t80) cc_final: 0.6777 (t80) REVERT: A 74 TYR cc_start: 0.7431 (t80) cc_final: 0.7183 (t80) REVERT: A 86 GLN cc_start: 0.8899 (mt0) cc_final: 0.8694 (mt0) REVERT: A 124 MET cc_start: 0.8398 (tpp) cc_final: 0.7439 (tpp) REVERT: A 152 MET cc_start: 0.8819 (tpp) cc_final: 0.7631 (tpt) REVERT: A 372 CYS cc_start: 0.8986 (m) cc_final: 0.8686 (m) REVERT: A 374 GLN cc_start: 0.8492 (mt0) cc_final: 0.7971 (mm-40) REVERT: A 434 ILE cc_start: 0.9380 (pt) cc_final: 0.8919 (pt) REVERT: A 514 ASP cc_start: 0.8344 (m-30) cc_final: 0.7885 (m-30) REVERT: A 520 MET cc_start: 0.8584 (mmm) cc_final: 0.8069 (mmm) REVERT: A 534 ASP cc_start: 0.8524 (t70) cc_final: 0.8138 (t0) REVERT: A 614 LYS cc_start: 0.8184 (tttt) cc_final: 0.7840 (mttp) REVERT: A 652 LYS cc_start: 0.8329 (tttt) cc_final: 0.8059 (mttm) REVERT: A 666 TYR cc_start: 0.7392 (t80) cc_final: 0.7102 (t80) REVERT: B 1 MET cc_start: 0.0372 (mmt) cc_final: -0.0165 (mtt) REVERT: B 4 GLU cc_start: 0.7008 (pm20) cc_final: 0.6688 (tm-30) REVERT: B 36 LEU cc_start: 0.8953 (tp) cc_final: 0.8484 (mm) REVERT: B 81 HIS cc_start: 0.8972 (m-70) cc_final: 0.8038 (m-70) REVERT: B 168 CYS cc_start: 0.9021 (m) cc_final: 0.8700 (m) REVERT: B 204 PHE cc_start: 0.7981 (t80) cc_final: 0.7756 (t80) REVERT: B 289 MET cc_start: 0.3717 (mmt) cc_final: 0.3292 (mmt) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.1783 time to fit residues: 80.6864 Evaluate side-chains 257 residues out of total 1046 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 27 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 761 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** B 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.155656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.124451 restraints weight = 21578.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.124356 restraints weight = 14446.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125538 restraints weight = 12469.627| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9804 Z= 0.292 Angle : 0.721 11.554 13287 Z= 0.368 Chirality : 0.044 0.183 1478 Planarity : 0.004 0.052 1642 Dihedral : 4.916 26.702 1277 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 12.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1140 helix: 1.06 (0.18), residues: 841 sheet: None (None), residues: 0 loop : -2.10 (0.36), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 169 HIS 0.009 0.002 HIS B 79 PHE 0.030 0.002 PHE C 88 TYR 0.020 0.002 TYR A 636 ARG 0.020 0.001 ARG C 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2169.66 seconds wall clock time: 39 minutes 47.99 seconds (2387.99 seconds total)