Starting phenix.real_space_refine on Mon Mar 11 04:21:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1j_40969/03_2024/8t1j_40969_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1j_40969/03_2024/8t1j_40969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1j_40969/03_2024/8t1j_40969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1j_40969/03_2024/8t1j_40969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1j_40969/03_2024/8t1j_40969_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1j_40969/03_2024/8t1j_40969_updated.pdb" } resolution = 2.7 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= 0.121 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 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 TYR 698": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 562": "CD1" <-> "CD2" "CE1" <-> "CE2" 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-5265/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 33.487 54.832 48.590 1.00 0.00 S ATOM 274 SG CYS A 331 33.594 52.036 51.805 1.00 0.00 S ATOM 3648 SG CYS B 326 36.099 54.944 52.568 1.00 0.00 S ATOM 3688 SG CYS B 331 36.316 52.165 49.106 1.00 0.00 S ATOM 965 SG CYS A 415 42.977 42.732 34.962 1.00 0.00 S ATOM 4379 SG CYS B 415 28.567 40.706 65.373 1.00 0.00 S Time building chain proxies: 4.38, per 1000 atoms: 0.63 Number of scatterers: 6973 At special positions: 0 Unit cell: (74.13, 83.661, 101.664, 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 1.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 331 " 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 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 38.1% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.44 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: 6.379A pdb=" N LYS A 452 " --> pdb=" O TYR A 448 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLY A 453 " --> pdb=" O ALA A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 508 removed outlier: 5.333A 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 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: 3.627A 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: 6.392A pdb=" N LYS B 452 " --> pdb=" O TYR B 448 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 508 removed outlier: 3.502A pdb=" N VAL B 499 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N GLN B 500 " --> pdb=" O ALA B 497 " (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 692 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 706 228 hydrogen bonds defined for protein. 588 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: 1.81 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.40: 2923 1.40 - 1.59: 4185 1.59 - 1.78: 2 1.78 - 1.98: 65 1.98 - 2.17: 5 Bond restraints: 7180 Sorted by residual: bond pdb=" C3B HEM B1503 " pdb=" CAB HEM B1503 " ideal model delta sigma weight residual 1.544 1.391 0.153 2.00e-02 2.50e+03 5.81e+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 5.03e+01 bond pdb=" C3C HEM A1504 " pdb=" CAC HEM A1504 " ideal model delta sigma weight residual 1.544 1.409 0.135 2.00e-02 2.50e+03 4.57e+01 bond pdb=" C4A H4B A1503 " pdb=" N5 H4B A1503 " ideal model delta sigma weight residual 1.368 1.465 -0.097 1.60e-02 3.91e+03 3.68e+01 ... (remaining 7175 not shown) Histogram of bond angle deviations from ideal: 87.27 - 102.91: 85 102.91 - 118.55: 5664 118.55 - 134.19: 4017 134.19 - 149.83: 0 149.83 - 165.47: 4 Bond angle restraints: 9770 Sorted by residual: angle pdb=" N LEU A 354 " pdb=" CA LEU A 354 " pdb=" C LEU A 354 " ideal model delta sigma weight residual 111.36 119.13 -7.77 1.09e+00 8.42e-01 5.08e+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 VAL B 499 " pdb=" CA VAL B 499 " pdb=" C VAL B 499 " ideal model delta sigma weight residual 110.42 116.18 -5.76 9.60e-01 1.09e+00 3.59e+01 angle pdb=" N1 H4B B1502 " pdb=" C2 H4B B1502 " pdb=" N3 H4B B1502 " ideal model delta sigma weight residual 123.14 117.15 5.99 1.00e+00 1.00e+00 3.59e+01 angle pdb=" N ASN A 712 " pdb=" CA ASN A 712 " pdb=" C ASN A 712 " ideal model delta sigma weight residual 113.17 105.66 7.51 1.26e+00 6.30e-01 3.55e+01 ... (remaining 9765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.64: 4088 21.64 - 43.28: 95 43.28 - 64.92: 29 64.92 - 86.56: 10 86.56 - 108.20: 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 -101.42 -78.58 2 1.00e+01 1.00e-02 4.61e+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 -118.80 -61.20 2 1.00e+01 1.00e-02 3.69e+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 180.00 151.45 28.55 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 4227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 676 0.070 - 0.139: 265 0.139 - 0.209: 56 0.209 - 0.278: 15 0.278 - 0.348: 2 Chirality restraints: 1014 Sorted by residual: chirality pdb=" CA VAL B 474 " pdb=" N VAL B 474 " pdb=" C VAL B 474 " pdb=" CB VAL B 474 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.02e+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 2.18 0.33 2.00e-01 2.50e+01 2.78e+00 chirality pdb=" CA ASP B 347 " pdb=" N ASP B 347 " pdb=" C ASP B 347 " pdb=" CB ASP B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 1011 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEM A1504 " 0.015 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 " -0.174 2.00e-02 2.50e+03 pdb=" CMA HEM A1504 " 0.162 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 " -0.136 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 2.28e+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 " -0.003 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 " -0.074 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: 2.50 - 2.98: 3435 2.98 - 3.46: 6759 3.46 - 3.94: 12183 3.94 - 4.42: 14745 4.42 - 4.90: 22161 Nonbonded interactions: 59283 Sorted by model distance: nonbonded pdb=" N ASN B 712 " pdb=" N THR B 713 " model vdw 2.502 2.560 nonbonded pdb=" N ASN A 712 " pdb=" N THR A 713 " model vdw 2.502 2.560 nonbonded pdb=" O THR B 433 " pdb=" ND2 ASN B 527 " model vdw 2.525 2.520 nonbonded pdb=" OE1 GLN B 478 " pdb=" NH1 ARG B 481 " model vdw 2.526 2.520 nonbonded pdb=" O THR A 433 " pdb=" ND2 ASN A 527 " model vdw 2.531 2.520 ... (remaining 59278 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: 1.630 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: 7.210 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 24.590 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 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 0.156 7180 Z= 0.772 Angle : 1.447 26.910 9770 Z= 0.969 Chirality : 0.075 0.348 1014 Planarity : 0.011 0.126 1240 Dihedral : 12.837 108.198 2646 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 0.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 0.15 (0.26), residues: 834 helix: -0.01 (0.26), residues: 296 sheet: 0.14 (0.56), residues: 78 loop : 0.33 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.006 TRP B 711 HIS 0.009 0.001 HIS B 714 PHE 0.035 0.003 PHE B 554 TYR 0.100 0.016 TYR A 604 ARG 0.008 0.001 ARG B 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 144 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.893 Fit side-chains REVERT: B 369 ILE cc_start: 0.7254 (pt) cc_final: 0.7049 (pt) REVERT: B 695 MET cc_start: 0.8951 (mtt) cc_final: 0.8687 (mtt) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 1.6018 time to fit residues: 239.9679 Evaluate side-chains 84 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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: 1.9990 chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN A 445 HIS A 525 GLN A 535 GLN B 353 GLN B 385 ASN B 642 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7180 Z= 0.221 Angle : 0.626 16.615 9770 Z= 0.293 Chirality : 0.042 0.134 1014 Planarity : 0.004 0.035 1240 Dihedral : 11.248 99.425 962 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.26 % Allowed : 8.91 % 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: 1.26 (0.28), residues: 834 helix: 1.33 (0.30), residues: 302 sheet: 0.03 (0.59), residues: 76 loop : 0.82 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 587 HIS 0.017 0.001 HIS B 714 PHE 0.014 0.002 PHE B 300 TYR 0.011 0.001 TYR A 366 ARG 0.004 0.000 ARG A 414 *********************** 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 105 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.907 Fit side-chains REVERT: A 550 LYS cc_start: 0.6867 (OUTLIER) cc_final: 0.6423 (tppt) REVERT: B 695 MET cc_start: 0.8995 (mtt) cc_final: 0.8732 (mtt) outliers start: 17 outliers final: 9 residues processed: 99 average time/residue: 1.5780 time to fit residues: 163.0183 Evaluate side-chains 83 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 351 LYS Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 668 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 66 optimal weight: 0.0980 chunk 73 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 507 GLN A 605 ASN A 692 HIS A 712 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7180 Z= 0.214 Angle : 0.600 16.466 9770 Z= 0.269 Chirality : 0.042 0.156 1014 Planarity : 0.004 0.040 1240 Dihedral : 10.784 97.394 962 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.93 % Allowed : 10.51 % Favored : 86.57 % 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: 1.21 (0.29), residues: 834 helix: 1.35 (0.30), residues: 302 sheet: -0.17 (0.59), residues: 76 loop : 0.78 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 587 HIS 0.013 0.001 HIS B 714 PHE 0.024 0.002 PHE A 355 TYR 0.010 0.001 TYR A 366 ARG 0.003 0.000 ARG A 414 *********************** 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 102 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.791 Fit side-chains REVERT: A 550 LYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6471 (tppt) REVERT: B 650 ASP cc_start: 0.7654 (OUTLIER) cc_final: 0.7452 (p0) outliers start: 22 outliers final: 7 residues processed: 96 average time/residue: 1.5044 time to fit residues: 151.0725 Evaluate side-chains 85 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 550 LYS Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 668 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 21 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN A 605 ASN A 712 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3093 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= 0.193 Angle : 0.551 14.075 9770 Z= 0.254 Chirality : 0.041 0.163 1014 Planarity : 0.004 0.042 1240 Dihedral : 10.405 92.636 962 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.13 % Allowed : 12.10 % Favored : 85.77 % 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: 1.15 (0.30), residues: 834 helix: 1.19 (0.31), residues: 306 sheet: 0.21 (0.55), residues: 96 loop : 0.76 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 587 HIS 0.012 0.001 HIS B 714 PHE 0.025 0.001 PHE B 355 TYR 0.008 0.001 TYR A 366 ARG 0.002 0.000 ARG A 414 *********************** 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 90 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 74 time to evaluate : 0.909 Fit side-chains REVERT: B 650 ASP cc_start: 0.7653 (OUTLIER) cc_final: 0.7404 (p0) outliers start: 16 outliers final: 8 residues processed: 87 average time/residue: 1.5457 time to fit residues: 140.6162 Evaluate side-chains 83 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 668 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN A 605 ASN A 712 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7180 Z= 0.284 Angle : 0.611 15.663 9770 Z= 0.277 Chirality : 0.043 0.140 1014 Planarity : 0.004 0.042 1240 Dihedral : 11.150 101.896 962 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.19 % Allowed : 11.57 % Favored : 85.24 % 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 (0.30), residues: 834 helix: 1.01 (0.30), residues: 306 sheet: 0.18 (0.56), residues: 96 loop : 0.59 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 678 HIS 0.011 0.001 HIS B 714 PHE 0.022 0.002 PHE B 355 TYR 0.010 0.001 TYR A 366 ARG 0.004 0.001 ARG B 481 *********************** 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 101 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 77 time to evaluate : 0.848 Fit side-chains revert: symmetry clash REVERT: B 650 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7545 (p0) outliers start: 24 outliers final: 15 residues processed: 93 average time/residue: 1.4946 time to fit residues: 145.3756 Evaluate side-chains 89 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 552 ASP Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain A residue 656 GLU Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 686 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 0.3980 chunk 79 optimal weight: 0.0470 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN A 605 ASN A 712 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7180 Z= 0.199 Angle : 0.545 13.242 9770 Z= 0.255 Chirality : 0.041 0.153 1014 Planarity : 0.004 0.043 1240 Dihedral : 10.577 95.512 962 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.53 % Allowed : 12.37 % Favored : 85.11 % 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 (0.30), residues: 834 helix: 1.07 (0.31), residues: 306 sheet: 0.20 (0.57), residues: 96 loop : 0.59 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 587 HIS 0.011 0.001 HIS B 714 PHE 0.022 0.001 PHE B 355 TYR 0.008 0.001 TYR B 366 ARG 0.004 0.000 ARG A 349 *********************** 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 93 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 0.865 Fit side-chains REVERT: B 650 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7459 (p0) outliers start: 19 outliers final: 12 residues processed: 89 average time/residue: 1.6398 time to fit residues: 152.6180 Evaluate side-chains 84 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 686 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 79 optimal weight: 0.0270 chunk 49 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 overall best weight: 1.1444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 601 ASN A 605 ASN A 712 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 7180 Z= 0.325 Angle : 0.623 15.152 9770 Z= 0.286 Chirality : 0.044 0.143 1014 Planarity : 0.004 0.043 1240 Dihedral : 11.324 102.375 962 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.66 % Allowed : 12.37 % Favored : 84.97 % 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: 0.71 (0.29), residues: 834 helix: 0.91 (0.30), residues: 306 sheet: 0.11 (0.56), residues: 96 loop : 0.40 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 678 HIS 0.010 0.002 HIS B 714 PHE 0.020 0.002 PHE B 355 TYR 0.010 0.001 TYR A 366 ARG 0.004 0.001 ARG A 349 *********************** 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 92 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.879 Fit side-chains outliers start: 20 outliers final: 16 residues processed: 87 average time/residue: 1.5190 time to fit residues: 138.3834 Evaluate side-chains 88 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 686 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS A 605 ASN A 712 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7180 Z= 0.255 Angle : 0.586 13.888 9770 Z= 0.274 Chirality : 0.042 0.141 1014 Planarity : 0.004 0.043 1240 Dihedral : 11.045 99.610 962 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.53 % Allowed : 12.90 % Favored : 84.57 % 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: 0.71 (0.29), residues: 834 helix: 0.94 (0.30), residues: 306 sheet: 0.05 (0.56), residues: 96 loop : 0.39 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 587 HIS 0.010 0.001 HIS B 714 PHE 0.038 0.002 PHE A 300 TYR 0.008 0.001 TYR A 366 ARG 0.007 0.000 ARG A 349 *********************** 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 90 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 0.903 Fit side-chains REVERT: B 650 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7556 (p0) outliers start: 19 outliers final: 15 residues processed: 85 average time/residue: 1.4719 time to fit residues: 131.2470 Evaluate side-chains 86 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 70 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 552 ASP Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 686 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 57 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS A 605 ASN A 712 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7180 Z= 0.219 Angle : 0.556 12.836 9770 Z= 0.261 Chirality : 0.042 0.141 1014 Planarity : 0.004 0.044 1240 Dihedral : 10.774 97.289 962 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.26 % Allowed : 12.63 % Favored : 85.11 % 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: 0.77 (0.29), residues: 834 helix: 1.00 (0.31), residues: 306 sheet: -0.45 (0.60), residues: 76 loop : 0.51 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 587 HIS 0.010 0.001 HIS B 714 PHE 0.034 0.002 PHE A 300 TYR 0.008 0.001 TYR B 366 ARG 0.008 0.000 ARG A 349 *********************** 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 92 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 75 time to evaluate : 0.791 Fit side-chains REVERT: B 650 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7511 (p0) outliers start: 17 outliers final: 15 residues processed: 89 average time/residue: 1.5307 time to fit residues: 142.8484 Evaluate side-chains 89 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 686 SER 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: 2.9990 chunk 81 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 19 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS A 605 ASN A 712 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7180 Z= 0.277 Angle : 0.594 14.110 9770 Z= 0.277 Chirality : 0.043 0.141 1014 Planarity : 0.004 0.043 1240 Dihedral : 10.993 100.115 962 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.13 % Allowed : 13.16 % Favored : 84.71 % 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: 0.70 (0.29), residues: 834 helix: 0.96 (0.31), residues: 306 sheet: -0.47 (0.60), residues: 76 loop : 0.44 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 306 HIS 0.010 0.001 HIS B 714 PHE 0.031 0.002 PHE A 300 TYR 0.009 0.001 TYR A 366 ARG 0.008 0.001 ARG A 349 ********************** 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 88 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.895 Fit side-chains REVERT: B 650 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7561 (p0) outliers start: 16 outliers final: 14 residues processed: 84 average time/residue: 1.5015 time to fit residues: 132.2944 Evaluate side-chains 87 residues out of total 752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 367 SER Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 612 LYS Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 650 ASP Chi-restraints excluded: chain B residue 668 CYS Chi-restraints excluded: chain B residue 686 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.0980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.0770 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS A 605 ASN A 712 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.125118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.098488 restraints weight = 8495.595| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.97 r_work: 0.3132 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3537 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= 0.175 Angle : 0.523 10.957 9770 Z= 0.249 Chirality : 0.041 0.170 1014 Planarity : 0.004 0.044 1240 Dihedral : 10.226 91.583 962 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.73 % Allowed : 13.70 % Favored : 84.57 % 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: 1.10 (0.31), residues: 306 sheet: -0.43 (0.60), residues: 76 loop : 0.58 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 587 HIS 0.010 0.001 HIS B 714 PHE 0.030 0.001 PHE A 300 TYR 0.008 0.001 TYR B 366 ARG 0.008 0.000 ARG A 349 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3044.84 seconds wall clock time: 54 minutes 33.14 seconds (3273.14 seconds total)