Starting phenix.real_space_refine on Sat Apr 6 04:11:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1k_40970/04_2024/8t1k_40970_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1k_40970/04_2024/8t1k_40970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1k_40970/04_2024/8t1k_40970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1k_40970/04_2024/8t1k_40970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1k_40970/04_2024/8t1k_40970_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1k_40970/04_2024/8t1k_40970_updated.pdb" } resolution = 3.14 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= -0.001 sd= 0.141 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 Zn 1 6.06 5 S 42 5.16 5 C 4460 2.51 5 N 1202 2.21 5 O 1266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 299": "NH1" <-> "NH2" Residue "A ARG 343": "NH1" <-> "NH2" Residue "A ARG 349": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A ARG 414": "NH1" <-> "NH2" Residue "A ARG 418": "NH1" <-> "NH2" Residue "A ARG 430": "NH1" <-> "NH2" Residue "A ARG 456": "NH1" <-> "NH2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "A ARG 473": "NH1" <-> "NH2" Residue "A ARG 481": "NH1" <-> "NH2" Residue "A ARG 514": "NH1" <-> "NH2" Residue "A ARG 516": "NH1" <-> "NH2" Residue "A ARG 547": "NH1" <-> "NH2" Residue "A TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 596": "NH1" <-> "NH2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 667": "NH1" <-> "NH2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 699": "NH1" <-> "NH2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B ARG 343": "NH1" <-> "NH2" Residue "B ARG 349": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 380": "NH1" <-> "NH2" Residue "B ARG 410": "NH1" <-> "NH2" Residue "B ARG 414": "NH1" <-> "NH2" Residue "B ARG 418": "NH1" <-> "NH2" Residue "B ARG 430": "NH1" <-> "NH2" Residue "B ARG 456": "NH1" <-> "NH2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "B ARG 473": "NH1" <-> "NH2" Residue "B ARG 481": "NH1" <-> "NH2" Residue "B ARG 514": "NH1" <-> "NH2" Residue "B ARG 516": "NH1" <-> "NH2" Residue "B ARG 547": "NH1" <-> "NH2" Residue "B ARG 596": "NH1" <-> "NH2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B ARG 667": "NH1" <-> "NH2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B ARG 699": "NH1" <-> "NH2" Residue "A ARG 1502": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 6973 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3414 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 396} Chain: "B" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3414 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 396} Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {' ZN': 1, 'H4B': 1, 'HEM': 1} Inner-chain residues flagged as termini: ['pdbres="ARG A1502 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'H4B': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 234 SG CYS A 326 36.136 27.320 47.401 1.00 0.00 S ATOM 274 SG CYS A 331 36.502 30.069 50.826 1.00 0.00 S ATOM 3648 SG CYS B 326 33.713 27.338 51.424 1.00 0.00 S ATOM 3688 SG CYS B 331 33.825 30.349 48.205 1.00 0.00 S ATOM 965 SG CYS A 415 29.189 41.684 34.489 1.00 0.00 S ATOM 4379 SG CYS B 415 43.340 39.579 64.879 1.00 0.00 S Time building chain proxies: 5.41, per 1000 atoms: 0.78 Number of scatterers: 6973 At special positions: 0 Unit cell: (74.784, 82.992, 101.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Fe 2 26.01 S 42 16.00 O 1266 8.00 N 1202 7.00 C 4460 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.86 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS B 331 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 326 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 331 " pdb="ZN ZN A1501 " - pdb=" SG CYS B 326 " Number of angles added : 6 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 12 sheets defined 38.0% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 351 through 368 Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 375 through 391 Processing helix chain 'A' and resid 398 through 410 Processing helix chain 'A' and resid 418 through 420 No H-bonds generated for 'chain 'A' and resid 418 through 420' Processing helix chain 'A' and resid 435 through 453 removed outlier: 6.383A pdb=" N LYS A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLY A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 508 removed outlier: 5.248A pdb=" N GLN A 500 " --> pdb=" O ALA A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 540 No H-bonds generated for 'chain 'A' and resid 538 through 540' Processing helix chain 'A' and resid 554 through 557 Processing helix chain 'A' and resid 590 through 594 Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 621 through 623 No H-bonds generated for 'chain 'A' and resid 621 through 623' Processing helix chain 'A' and resid 625 through 643 Processing helix chain 'A' and resid 651 through 668 removed outlier: 3.586A pdb=" N THR A 655 " --> pdb=" O HIS A 651 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 679 No H-bonds generated for 'chain 'A' and resid 676 through 679' Processing helix chain 'A' and resid 685 through 687 No H-bonds generated for 'chain 'A' and resid 685 through 687' Processing helix chain 'A' and resid 689 through 692 removed outlier: 3.647A pdb=" N HIS A 692 " --> pdb=" O PRO A 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 689 through 692' Processing helix chain 'A' and resid 710 through 712 No H-bonds generated for 'chain 'A' and resid 710 through 712' Processing helix chain 'B' and resid 316 through 319 Processing helix chain 'B' and resid 351 through 368 Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 375 through 391 Processing helix chain 'B' and resid 398 through 410 Processing helix chain 'B' and resid 418 through 420 No H-bonds generated for 'chain 'B' and resid 418 through 420' Processing helix chain 'B' and resid 435 through 453 removed outlier: 6.209A pdb=" N LYS B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N GLY B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 508 removed outlier: 5.290A pdb=" N GLN B 500 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR B 502 " --> pdb=" O VAL B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 540 No H-bonds generated for 'chain 'B' and resid 538 through 540' Processing helix chain 'B' and resid 554 through 557 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 613 Processing helix chain 'B' and resid 621 through 623 No H-bonds generated for 'chain 'B' and resid 621 through 623' Processing helix chain 'B' and resid 625 through 643 Processing helix chain 'B' and resid 651 through 668 Processing helix chain 'B' and resid 676 through 679 No H-bonds generated for 'chain 'B' and resid 676 through 679' Processing helix chain 'B' and resid 685 through 687 No H-bonds generated for 'chain 'B' and resid 685 through 687' Processing helix chain 'B' and resid 689 through 691 No H-bonds generated for 'chain 'B' and resid 689 through 691' Processing helix chain 'B' and resid 710 through 712 No H-bonds generated for 'chain 'B' and resid 710 through 712' Processing sheet with id= A, first strand: chain 'A' and resid 301 through 304 Processing sheet with id= B, first strand: chain 'A' and resid 425 through 429 Processing sheet with id= C, first strand: chain 'A' and resid 484 through 486 Processing sheet with id= D, first strand: chain 'A' and resid 522 through 524 Processing sheet with id= E, first strand: chain 'A' and resid 543 through 545 Processing sheet with id= F, first strand: chain 'A' and resid 703 through 706 Processing sheet with id= G, first strand: chain 'B' and resid 301 through 304 Processing sheet with id= H, first strand: chain 'B' and resid 425 through 429 Processing sheet with id= I, first strand: chain 'B' and resid 484 through 486 Processing sheet with id= J, first strand: chain 'B' and resid 522 through 524 Processing sheet with id= K, first strand: chain 'B' and resid 543 through 545 Processing sheet with id= L, first strand: chain 'B' and resid 703 through 706 226 hydrogen bonds defined for protein. 585 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: 1.96 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.35: 2195 1.35 - 1.55: 4911 1.55 - 1.76: 4 1.76 - 1.96: 65 1.96 - 2.17: 5 Bond restraints: 7180 Sorted by residual: bond pdb=" C TYR B 588 " pdb=" O TYR B 588 " ideal model delta sigma weight residual 1.235 1.141 0.094 1.18e-02 7.18e+03 6.35e+01 bond pdb=" CA TYR B 588 " pdb=" C TYR B 588 " ideal model delta sigma weight residual 1.523 1.424 0.099 1.24e-02 6.50e+03 6.31e+01 bond pdb=" C3B HEM B1503 " pdb=" CAB HEM B1503 " ideal model delta sigma weight residual 1.544 1.393 0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" C3B HEM A1504 " pdb=" CAB HEM A1504 " ideal model delta sigma weight residual 1.544 1.394 0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" C3C HEM B1503 " pdb=" CAC HEM B1503 " ideal model delta sigma weight residual 1.544 1.402 0.142 2.00e-02 2.50e+03 5.07e+01 ... (remaining 7175 not shown) Histogram of bond angle deviations from ideal: 87.30 - 102.93: 91 102.93 - 118.57: 5667 118.57 - 134.20: 4008 134.20 - 149.83: 0 149.83 - 165.46: 4 Bond angle restraints: 9770 Sorted by residual: angle pdb=" CA TYR B 588 " pdb=" C TYR B 588 " pdb=" O TYR B 588 " ideal model delta sigma weight residual 120.80 111.77 9.03 1.11e+00 8.12e-01 6.62e+01 angle pdb=" N LEU B 354 " pdb=" CA LEU B 354 " pdb=" C LEU B 354 " ideal model delta sigma weight residual 111.36 119.12 -7.76 1.09e+00 8.42e-01 5.07e+01 angle pdb=" N LEU A 354 " pdb=" CA LEU A 354 " pdb=" C LEU A 354 " ideal model delta sigma weight residual 111.36 119.06 -7.70 1.09e+00 8.42e-01 4.99e+01 angle pdb=" N ASN A 712 " pdb=" CA ASN A 712 " pdb=" C ASN A 712 " ideal model delta sigma weight residual 113.17 105.57 7.60 1.26e+00 6.30e-01 3.64e+01 angle pdb=" N ASN B 712 " pdb=" CA ASN B 712 " pdb=" C ASN B 712 " ideal model delta sigma weight residual 113.17 105.62 7.55 1.26e+00 6.30e-01 3.59e+01 ... (remaining 9765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 4086 21.63 - 43.27: 99 43.27 - 64.90: 26 64.90 - 86.54: 11 86.54 - 108.17: 8 Dihedral angle restraints: 4230 sinusoidal: 1778 harmonic: 2452 Sorted by residual: dihedral pdb=" C2B HEM A1504 " pdb=" C3B HEM A1504 " pdb=" CAB HEM A1504 " pdb=" CBB HEM A1504 " ideal model delta sinusoidal sigma weight residual -180.00 -106.49 -73.51 2 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" C2B HEM B1503 " pdb=" C3B HEM B1503 " pdb=" CAB HEM B1503 " pdb=" CBB HEM B1503 " ideal model delta sinusoidal sigma weight residual -180.00 -117.70 -62.30 2 1.00e+01 1.00e-02 3.76e+01 dihedral pdb=" CA TYR A 588 " pdb=" C TYR A 588 " pdb=" N MET A 589 " pdb=" CA MET A 589 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 4227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 709 0.076 - 0.152: 258 0.152 - 0.228: 40 0.228 - 0.304: 5 0.304 - 0.380: 2 Chirality restraints: 1014 Sorted by residual: chirality pdb=" CA ASP A 471 " pdb=" N ASP A 471 " pdb=" C ASP A 471 " pdb=" CB ASP A 471 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CA VAL A 474 " pdb=" N VAL A 474 " pdb=" C VAL A 474 " pdb=" CB VAL A 474 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA ASP B 471 " pdb=" N ASP B 471 " pdb=" C ASP B 471 " pdb=" CB ASP B 471 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1011 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEM A1504 " -0.016 2.00e-02 2.50e+03 1.26e-01 3.55e+02 pdb=" C2A HEM A1504 " -0.038 2.00e-02 2.50e+03 pdb=" C3A HEM A1504 " -0.104 2.00e-02 2.50e+03 pdb=" C4A HEM A1504 " -0.015 2.00e-02 2.50e+03 pdb=" CAA HEM A1504 " 0.251 2.00e-02 2.50e+03 pdb=" CHA HEM A1504 " -0.100 2.00e-02 2.50e+03 pdb=" CHB HEM A1504 " 0.173 2.00e-02 2.50e+03 pdb=" CMA HEM A1504 " -0.161 2.00e-02 2.50e+03 pdb=" NA HEM A1504 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND HEM B1503 " -0.137 2.00e-02 2.50e+03 1.08e-01 2.62e+02 pdb=" C1D HEM B1503 " -0.147 2.00e-02 2.50e+03 pdb=" C2D HEM B1503 " -0.080 2.00e-02 2.50e+03 pdb=" C3D HEM B1503 " -0.024 2.00e-02 2.50e+03 pdb=" C4D HEM B1503 " -0.002 2.00e-02 2.50e+03 pdb=" CAD HEM B1503 " -0.003 2.00e-02 2.50e+03 pdb=" CHA HEM B1503 " 0.145 2.00e-02 2.50e+03 pdb=" CHD HEM B1503 " 0.179 2.00e-02 2.50e+03 pdb=" CMD HEM B1503 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM A1504 " -0.164 2.00e-02 2.50e+03 1.01e-01 2.27e+02 pdb=" C1B HEM A1504 " -0.019 2.00e-02 2.50e+03 pdb=" C2B HEM A1504 " 0.013 2.00e-02 2.50e+03 pdb=" C3B HEM A1504 " 0.002 2.00e-02 2.50e+03 pdb=" C4B HEM A1504 " -0.071 2.00e-02 2.50e+03 pdb=" CAB HEM A1504 " 0.092 2.00e-02 2.50e+03 pdb=" CHB HEM A1504 " 0.181 2.00e-02 2.50e+03 pdb=" CHC HEM A1504 " 0.073 2.00e-02 2.50e+03 pdb=" CMB HEM A1504 " -0.108 2.00e-02 2.50e+03 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 2287 2.86 - 3.37: 6488 3.37 - 3.88: 11952 3.88 - 4.39: 14926 4.39 - 4.90: 23450 Nonbonded interactions: 59103 Sorted by model distance: nonbonded pdb=" N TYR B 588 " pdb=" O TYR B 588 " model vdw 2.350 2.496 nonbonded pdb=" NZ LYS B 359 " pdb=" OD2 ASP B 363 " model vdw 2.434 2.520 nonbonded pdb=" OE1 GLN B 478 " pdb=" NH1 ARG B 481 " model vdw 2.469 2.520 nonbonded pdb=" O THR A 433 " pdb=" ND2 ASN A 527 " model vdw 2.493 2.520 nonbonded pdb=" N ASN B 712 " pdb=" N THR B 713 " model vdw 2.502 2.560 ... (remaining 59098 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 298 through 716 or resid 1502 through 1504)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 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: 0.000 Extract box with map and model: 8.430 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.510 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 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 : 0.012 0.154 7180 Z= 0.792 Angle : 1.456 26.935 9770 Z= 0.978 Chirality : 0.074 0.380 1014 Planarity : 0.009 0.126 1240 Dihedral : 12.821 108.170 2646 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 4.55 % 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: 0.05 (0.26), residues: 834 helix: -0.17 (0.26), residues: 296 sheet: 0.10 (0.54), residues: 76 loop : 0.34 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.006 TRP A 676 HIS 0.004 0.000 HIS B 470 PHE 0.035 0.003 PHE B 554 TYR 0.100 0.014 TYR B 604 ARG 0.008 0.001 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.797 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2582 time to fit residues: 44.9712 Evaluate side-chains 80 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 0.7980 chunk 62 optimal weight: 0.1980 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN A 642 GLN B 454 ASN B 487 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7180 Z= 0.212 Angle : 0.591 16.027 9770 Z= 0.284 Chirality : 0.042 0.135 1014 Planarity : 0.004 0.036 1240 Dihedral : 10.993 94.380 962 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.93 % Allowed : 6.25 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.14 (0.28), residues: 834 helix: 1.29 (0.30), residues: 298 sheet: -0.04 (0.55), residues: 78 loop : 0.71 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 625 HIS 0.004 0.001 HIS A 714 PHE 0.016 0.002 PHE A 355 TYR 0.012 0.001 TYR B 366 ARG 0.004 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.737 Fit side-chains REVERT: A 328 GLU cc_start: 0.7461 (mp0) cc_final: 0.7212 (mp0) REVERT: B 328 GLU cc_start: 0.7743 (mp0) cc_final: 0.7541 (mp0) outliers start: 7 outliers final: 4 residues processed: 85 average time/residue: 0.2499 time to fit residues: 27.2408 Evaluate side-chains 71 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 MET Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 701 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 61 optimal weight: 0.0980 chunk 50 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 0.0980 chunk 66 optimal weight: 8.9990 chunk 73 optimal weight: 0.1980 chunk 25 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7180 Z= 0.177 Angle : 0.529 14.146 9770 Z= 0.249 Chirality : 0.041 0.175 1014 Planarity : 0.004 0.037 1240 Dihedral : 9.807 87.641 962 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.46 % Allowed : 6.78 % Favored : 91.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.24 (0.29), residues: 834 helix: 1.45 (0.31), residues: 298 sheet: -0.12 (0.56), residues: 78 loop : 0.74 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 625 HIS 0.004 0.001 HIS A 445 PHE 0.014 0.001 PHE B 355 TYR 0.009 0.001 TYR B 366 ARG 0.006 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.829 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 81 average time/residue: 0.2391 time to fit residues: 25.2735 Evaluate side-chains 77 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 701 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 79 optimal weight: 0.0670 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 21 optimal weight: 0.0570 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7180 Z= 0.195 Angle : 0.536 14.650 9770 Z= 0.248 Chirality : 0.042 0.189 1014 Planarity : 0.004 0.039 1240 Dihedral : 8.920 81.418 962 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.60 % Allowed : 6.91 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.10 (0.29), residues: 834 helix: 1.27 (0.30), residues: 302 sheet: 0.23 (0.54), residues: 96 loop : 0.62 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 625 HIS 0.004 0.001 HIS B 651 PHE 0.016 0.001 PHE A 355 TYR 0.009 0.001 TYR A 366 ARG 0.005 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.813 Fit side-chains REVERT: A 353 GLN cc_start: 0.8215 (mt0) cc_final: 0.7951 (mt0) outliers start: 12 outliers final: 7 residues processed: 84 average time/residue: 0.2331 time to fit residues: 25.5272 Evaluate side-chains 78 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 71 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 5.9990 chunk 44 optimal weight: 0.0050 chunk 1 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 chunk 40 optimal weight: 0.0060 chunk 71 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.5210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS A 507 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7180 Z= 0.196 Angle : 0.523 13.226 9770 Z= 0.243 Chirality : 0.042 0.189 1014 Planarity : 0.004 0.040 1240 Dihedral : 8.766 79.102 962 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.46 % Allowed : 8.51 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.04 (0.29), residues: 834 helix: 1.21 (0.31), residues: 302 sheet: 0.15 (0.54), residues: 96 loop : 0.60 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 587 HIS 0.004 0.001 HIS B 651 PHE 0.013 0.001 PHE A 355 TYR 0.008 0.001 TYR A 366 ARG 0.004 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.773 Fit side-chains REVERT: A 328 GLU cc_start: 0.7406 (mp0) cc_final: 0.7174 (mp0) REVERT: A 353 GLN cc_start: 0.8204 (mt0) cc_final: 0.7963 (mt0) outliers start: 11 outliers final: 11 residues processed: 82 average time/residue: 0.2456 time to fit residues: 26.1099 Evaluate side-chains 80 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 352 ASP Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 539 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 79 optimal weight: 0.0170 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.8020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS B 692 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7180 Z= 0.261 Angle : 0.576 15.814 9770 Z= 0.262 Chirality : 0.043 0.181 1014 Planarity : 0.004 0.040 1240 Dihedral : 9.455 85.923 962 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.73 % Allowed : 8.38 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.81 (0.29), residues: 834 helix: 1.01 (0.30), residues: 306 sheet: -0.01 (0.53), residues: 96 loop : 0.49 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 587 HIS 0.005 0.001 HIS B 651 PHE 0.012 0.002 PHE A 658 TYR 0.008 0.001 TYR A 366 ARG 0.002 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 72 time to evaluate : 0.824 Fit side-chains REVERT: A 353 GLN cc_start: 0.8210 (mt0) cc_final: 0.7975 (mt0) outliers start: 13 outliers final: 11 residues processed: 81 average time/residue: 0.2400 time to fit residues: 25.6609 Evaluate side-chains 82 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 539 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.5980 chunk 57 optimal weight: 0.9980 chunk 44 optimal weight: 0.4980 chunk 66 optimal weight: 0.0970 chunk 79 optimal weight: 0.0060 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7180 Z= 0.180 Angle : 0.505 10.544 9770 Z= 0.240 Chirality : 0.041 0.189 1014 Planarity : 0.004 0.040 1240 Dihedral : 8.691 79.269 962 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.46 % Allowed : 9.31 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.91 (0.29), residues: 834 helix: 1.07 (0.31), residues: 306 sheet: 0.04 (0.54), residues: 96 loop : 0.57 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 587 HIS 0.004 0.001 HIS A 445 PHE 0.014 0.001 PHE A 355 TYR 0.008 0.001 TYR A 366 ARG 0.003 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.812 Fit side-chains REVERT: A 353 GLN cc_start: 0.8176 (mt0) cc_final: 0.7969 (mt0) outliers start: 11 outliers final: 9 residues processed: 80 average time/residue: 0.2319 time to fit residues: 24.5255 Evaluate side-chains 81 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 539 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 62 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 73 optimal weight: 0.0030 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7180 Z= 0.207 Angle : 0.533 12.885 9770 Z= 0.249 Chirality : 0.042 0.188 1014 Planarity : 0.004 0.040 1240 Dihedral : 8.739 78.765 962 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.33 % Allowed : 9.57 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.89 (0.29), residues: 834 helix: 1.02 (0.31), residues: 306 sheet: 0.01 (0.54), residues: 96 loop : 0.59 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 587 HIS 0.005 0.001 HIS B 651 PHE 0.012 0.001 PHE A 355 TYR 0.008 0.001 TYR A 366 ARG 0.003 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 72 time to evaluate : 0.816 Fit side-chains REVERT: A 353 GLN cc_start: 0.8208 (mt0) cc_final: 0.7987 (mt0) outliers start: 10 outliers final: 10 residues processed: 79 average time/residue: 0.2504 time to fit residues: 25.7602 Evaluate side-chains 80 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 539 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.0570 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7180 Z= 0.204 Angle : 0.527 11.850 9770 Z= 0.247 Chirality : 0.042 0.189 1014 Planarity : 0.004 0.040 1240 Dihedral : 8.673 78.016 962 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.33 % Allowed : 10.11 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.93 (0.29), residues: 834 helix: 1.03 (0.31), residues: 306 sheet: 0.05 (0.54), residues: 96 loop : 0.63 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 587 HIS 0.004 0.001 HIS B 651 PHE 0.014 0.001 PHE A 355 TYR 0.008 0.001 TYR A 366 ARG 0.003 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.754 Fit side-chains REVERT: A 353 GLN cc_start: 0.8213 (mt0) cc_final: 0.7990 (mt0) outliers start: 10 outliers final: 10 residues processed: 76 average time/residue: 0.2377 time to fit residues: 23.8863 Evaluate side-chains 79 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 539 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 chunk 69 optimal weight: 0.5980 chunk 19 optimal weight: 0.0000 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7180 Z= 0.215 Angle : 0.542 13.056 9770 Z= 0.252 Chirality : 0.042 0.188 1014 Planarity : 0.004 0.040 1240 Dihedral : 8.802 79.269 962 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.33 % Allowed : 9.97 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.92 (0.29), residues: 834 helix: 1.01 (0.31), residues: 306 sheet: 0.05 (0.54), residues: 96 loop : 0.63 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 587 HIS 0.004 0.001 HIS B 651 PHE 0.013 0.001 PHE A 355 TYR 0.008 0.001 TYR A 366 ARG 0.002 0.000 ARG B 667 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 68 time to evaluate : 0.841 Fit side-chains REVERT: A 353 GLN cc_start: 0.8208 (mt0) cc_final: 0.7982 (mt0) outliers start: 10 outliers final: 10 residues processed: 75 average time/residue: 0.2474 time to fit residues: 24.5583 Evaluate side-chains 77 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 539 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.0670 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.107129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.084731 restraints weight = 7795.999| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 1.51 r_work: 0.2647 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7180 Z= 0.200 Angle : 0.524 11.752 9770 Z= 0.246 Chirality : 0.042 0.189 1014 Planarity : 0.004 0.040 1240 Dihedral : 8.610 77.117 962 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.46 % Allowed : 9.71 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.95 (0.29), residues: 834 helix: 1.04 (0.31), residues: 306 sheet: 0.08 (0.54), residues: 96 loop : 0.64 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 587 HIS 0.004 0.001 HIS B 651 PHE 0.013 0.001 PHE A 355 TYR 0.008 0.001 TYR A 366 ARG 0.002 0.000 ARG B 667 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1859.10 seconds wall clock time: 34 minutes 30.18 seconds (2070.18 seconds total)