Starting phenix.real_space_refine on Sat Dec 28 01:10:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t1j_40969/12_2024/8t1j_40969.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t1j_40969/12_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/cci-nas-00/data/ceres_data/8t1j_40969/12_2024/8t1j_40969.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t1j_40969/12_2024/8t1j_40969.map" model { file = "/net/cci-nas-00/data/ceres_data/8t1j_40969/12_2024/8t1j_40969.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t1j_40969/12_2024/8t1j_40969.cif" } 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. Time to flip 47 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 4.99, per 1000 atoms: 0.72 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 - 3.00 Amino acid : True - 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: 1.84 Conformation dependent library (CDL) restraints added in 1.1 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... Secondary structure from input PDB file: 36 helices and 16 sheets defined 44.8% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 315 through 320 Processing helix chain 'A' and resid 350 through 369 Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 374 through 392 Processing helix chain 'A' and resid 397 through 411 Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 434 through 451 Processing helix chain 'A' and resid 452 through 454 No H-bonds generated for 'chain 'A' and resid 452 through 454' Processing helix chain 'A' and resid 498 through 507 Processing helix chain 'A' and resid 537 through 541 Processing helix chain 'A' and resid 553 through 558 Processing helix chain 'A' and resid 590 through 595 Processing helix chain 'A' and resid 606 through 614 Processing helix chain 'A' and resid 620 through 623 Processing helix chain 'A' and resid 624 through 644 Processing helix chain 'A' and resid 650 through 669 Processing helix chain 'A' and resid 675 through 680 Processing helix chain 'A' and resid 684 through 693 Proline residue: A 689 - end of helix removed outlier: 3.627A pdb=" N HIS A 692 " --> pdb=" O PRO A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 713 Processing helix chain 'B' and resid 315 through 320 Processing helix chain 'B' and resid 350 through 369 Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 374 through 392 Processing helix chain 'B' and resid 397 through 411 Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 434 through 451 Processing helix chain 'B' and resid 452 through 454 No H-bonds generated for 'chain 'B' and resid 452 through 454' Processing helix chain 'B' and resid 498 through 507 Processing helix chain 'B' and resid 537 through 541 Processing helix chain 'B' and resid 553 through 558 Processing helix chain 'B' and resid 590 through 595 Processing helix chain 'B' and resid 606 through 614 Processing helix chain 'B' and resid 620 through 623 Processing helix chain 'B' and resid 624 through 644 Processing helix chain 'B' and resid 650 through 669 Processing helix chain 'B' and resid 675 through 680 Processing helix chain 'B' and resid 684 through 693 removed outlier: 3.508A pdb=" N ILE B 687 " --> pdb=" O SER B 684 " (cutoff:3.500A) Proline residue: B 689 - end of helix Processing helix chain 'B' and resid 709 through 713 Processing sheet with id=AA1, first strand: chain 'A' and resid 301 through 304 Processing sheet with id=AA2, first strand: chain 'A' and resid 330 through 331 Processing sheet with id=AA3, first strand: chain 'A' and resid 425 through 428 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'A' and resid 484 through 486 Processing sheet with id=AA6, first strand: chain 'A' and resid 543 through 545 Processing sheet with id=AA7, first strand: chain 'A' and resid 577 through 579 Processing sheet with id=AA8, first strand: chain 'A' and resid 588 through 589 removed outlier: 6.470A pdb=" N TYR A 588 " --> pdb=" O VAL A 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 697 through 698 Processing sheet with id=AB1, first strand: chain 'B' and resid 301 through 304 Processing sheet with id=AB2, first strand: chain 'B' and resid 425 through 428 Processing sheet with id=AB3, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AB4, first strand: chain 'B' and resid 484 through 486 Processing sheet with id=AB5, first strand: chain 'B' and resid 543 through 545 Processing sheet with id=AB6, first strand: chain 'B' and resid 577 through 579 Processing sheet with id=AB7, first strand: chain 'B' and resid 588 through 589 removed outlier: 6.526A pdb=" N TYR B 588 " --> pdb=" O VAL B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 296 hydrogen bonds defined for protein. 732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 2.08 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: 0.00 - 5.38: 9692 5.38 - 10.76: 74 10.76 - 16.15: 2 16.15 - 21.53: 0 21.53 - 26.91: 2 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: 3409 2.98 - 3.46: 6712 3.46 - 3.94: 12102 3.94 - 4.42: 14631 4.42 - 4.90: 22157 Nonbonded interactions: 59011 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 3.120 nonbonded pdb=" OE1 GLN B 478 " pdb=" NH1 ARG B 481 " model vdw 2.526 3.120 nonbonded pdb=" O THR A 433 " pdb=" ND2 ASN A 527 " model vdw 2.531 3.120 ... (remaining 59006 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 2.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.580 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.730 ------------------------------------------------------------------------------- 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= 0.753 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 to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.783 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: 1.6730 time to fit residues: 250.4621 Evaluate side-chains 84 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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: 0.9980 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 525 GLN A 535 GLN B 353 GLN B 385 ASN ** B 525 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 642 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 7180 Z= 0.242 Angle : 0.648 17.444 9770 Z= 0.309 Chirality : 0.043 0.136 1014 Planarity : 0.004 0.035 1240 Dihedral : 11.526 100.924 962 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.39 % Allowed : 8.24 % Favored : 89.36 % 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: 1.31 (0.29), residues: 834 helix: 1.34 (0.30), residues: 314 sheet: 0.10 (0.62), residues: 76 loop : 0.85 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 711 HIS 0.017 0.001 HIS B 714 PHE 0.015 0.002 PHE B 300 TYR 0.012 0.002 TYR A 366 ARG 0.005 0.001 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 110 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.822 Fit side-chains revert: symmetry clash REVERT: A 550 LYS cc_start: 0.6869 (OUTLIER) cc_final: 0.6424 (tppt) REVERT: B 573 GLU cc_start: 0.6378 (OUTLIER) cc_final: 0.6038 (tt0) REVERT: B 695 MET cc_start: 0.8913 (mtt) cc_final: 0.8655 (mtt) outliers start: 18 outliers final: 8 residues processed: 101 average time/residue: 1.5900 time to fit residues: 167.6058 Evaluate side-chains 88 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 507 GLN 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 371 ARG Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 573 GLU 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: 0.0770 chunk 61 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 GLN A 605 ASN A 712 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2805 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= 0.210 Angle : 0.593 16.044 9770 Z= 0.278 Chirality : 0.042 0.136 1014 Planarity : 0.004 0.038 1240 Dihedral : 10.982 96.461 962 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.13 % Allowed : 10.51 % Favored : 87.37 % 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: 1.42 (0.30), residues: 834 helix: 1.54 (0.30), residues: 310 sheet: 0.44 (0.57), residues: 96 loop : 0.78 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 587 HIS 0.012 0.001 HIS B 714 PHE 0.030 0.002 PHE A 355 TYR 0.009 0.001 TYR B 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 99 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.815 Fit side-chains outliers start: 16 outliers final: 7 residues processed: 92 average time/residue: 1.6390 time to fit residues: 157.4141 Evaluate side-chains 84 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 602 SER 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: 0.6980 chunk 56 optimal weight: 0.0870 chunk 38 optimal weight: 0.6980 chunk 8 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 0.3980 chunk 39 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- 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: 0.7694 moved from start: 0.3037 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= 0.198 Angle : 0.559 14.116 9770 Z= 0.265 Chirality : 0.041 0.137 1014 Planarity : 0.004 0.039 1240 Dihedral : 10.597 93.622 962 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.13 % Allowed : 11.70 % Favored : 86.17 % 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: 1.37 (0.30), residues: 834 helix: 1.48 (0.30), residues: 310 sheet: 0.41 (0.56), residues: 96 loop : 0.78 (0.31), residues: 428 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 0.039 0.002 PHE B 355 TYR 0.009 0.001 TYR B 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 98 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.798 Fit side-chains REVERT: A 550 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6512 (tppt) outliers start: 16 outliers final: 8 residues processed: 94 average time/residue: 1.6397 time to fit residues: 161.0138 Evaluate side-chains 87 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 507 GLN 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 368 SER Chi-restraints excluded: chain B residue 602 SER 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: 0.1980 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 0.0980 chunk 32 optimal weight: 0.8980 chunk 67 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 HIS A 601 ASN A 605 ASN A 712 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3137 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= 0.200 Angle : 0.551 13.549 9770 Z= 0.262 Chirality : 0.041 0.155 1014 Planarity : 0.004 0.039 1240 Dihedral : 10.454 93.518 962 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.46 % Allowed : 12.90 % Favored : 85.64 % 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: 1.36 (0.30), residues: 834 helix: 1.41 (0.30), residues: 314 sheet: 0.43 (0.56), residues: 96 loop : 0.81 (0.32), residues: 424 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 B 355 TYR 0.009 0.001 TYR B 366 ARG 0.006 0.000 ARG A 371 *********************** 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 87 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.664 Fit side-chains outliers start: 11 outliers final: 8 residues processed: 82 average time/residue: 1.3687 time to fit residues: 117.2500 Evaluate side-chains 82 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 668 CYS 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: 0.3980 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 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: 1.2386 ------------------------------------------------------------------------------- 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 692 HIS A 712 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 7180 Z= 0.363 Angle : 0.660 16.464 9770 Z= 0.305 Chirality : 0.045 0.139 1014 Planarity : 0.004 0.039 1240 Dihedral : 11.530 104.248 962 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.39 % Allowed : 11.97 % Favored : 85.64 % 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: 1.00 (0.29), residues: 834 helix: 1.07 (0.29), residues: 318 sheet: 0.33 (0.56), residues: 96 loop : 0.60 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 678 HIS 0.009 0.002 HIS B 714 PHE 0.039 0.003 PHE B 355 TYR 0.011 0.002 TYR A 366 ARG 0.006 0.001 ARG A 371 *********************** 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 97 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.855 Fit side-chains outliers start: 18 outliers final: 14 residues processed: 93 average time/residue: 1.3926 time to fit residues: 135.4013 Evaluate side-chains 90 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 507 GLN 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 368 SER Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 491 SER Chi-restraints excluded: chain B residue 602 SER 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 0.0670 chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS A 601 ASN A 605 ASN A 712 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3371 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= 0.228 Angle : 0.578 13.609 9770 Z= 0.280 Chirality : 0.042 0.141 1014 Planarity : 0.004 0.041 1240 Dihedral : 11.016 97.813 962 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.26 % Allowed : 12.90 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.13 (0.30), residues: 834 helix: 1.31 (0.30), residues: 314 sheet: 0.31 (0.55), residues: 96 loop : 0.59 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 587 HIS 0.009 0.001 HIS B 714 PHE 0.041 0.002 PHE B 355 TYR 0.009 0.001 TYR A 698 ARG 0.006 0.000 ARG A 371 *********************** 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 to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.837 Fit side-chains outliers start: 17 outliers final: 10 residues processed: 86 average time/residue: 1.6282 time to fit residues: 146.3915 Evaluate side-chains 83 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 668 CYS 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: 2.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 75 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN A 712 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7180 Z= 0.252 Angle : 0.589 14.143 9770 Z= 0.281 Chirality : 0.043 0.135 1014 Planarity : 0.004 0.041 1240 Dihedral : 11.018 99.904 962 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.73 % Allowed : 13.43 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: 1.07 (0.29), residues: 834 helix: 1.29 (0.29), residues: 314 sheet: 0.32 (0.55), residues: 96 loop : 0.52 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 587 HIS 0.009 0.001 HIS B 714 PHE 0.040 0.002 PHE B 355 TYR 0.009 0.001 TYR B 366 ARG 0.007 0.000 ARG A 371 *********************** 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 86 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.812 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 82 average time/residue: 1.6952 time to fit residues: 145.0897 Evaluate side-chains 81 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 602 SER Chi-restraints excluded: chain B residue 622 SER Chi-restraints excluded: chain B residue 668 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN A 712 ASN B 642 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7180 Z= 0.278 Angle : 0.611 14.449 9770 Z= 0.292 Chirality : 0.043 0.138 1014 Planarity : 0.004 0.041 1240 Dihedral : 11.100 100.760 962 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.60 % Allowed : 13.70 % 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: 0.98 (0.29), residues: 834 helix: 1.15 (0.29), residues: 318 sheet: 0.31 (0.55), residues: 96 loop : 0.51 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 587 HIS 0.009 0.001 HIS B 714 PHE 0.043 0.002 PHE B 355 TYR 0.009 0.001 TYR B 366 ARG 0.008 0.001 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 89 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.854 Fit side-chains outliers start: 12 outliers final: 11 residues processed: 85 average time/residue: 1.5980 time to fit residues: 141.9693 Evaluate side-chains 85 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 489 ASP Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 602 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN A 712 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 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 : 0.004 0.052 7180 Z= 0.265 Angle : 0.601 14.119 9770 Z= 0.288 Chirality : 0.043 0.138 1014 Planarity : 0.004 0.041 1240 Dihedral : 11.066 100.461 962 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.33 % Allowed : 14.10 % 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: 0.98 (0.29), residues: 834 helix: 1.16 (0.29), residues: 318 sheet: 0.30 (0.54), residues: 96 loop : 0.50 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 587 HIS 0.009 0.001 HIS B 714 PHE 0.046 0.002 PHE B 355 TYR 0.009 0.001 TYR B 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 85 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.884 Fit side-chains outliers start: 10 outliers final: 10 residues processed: 82 average time/residue: 1.6062 time to fit residues: 137.9616 Evaluate side-chains 80 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 460 THR Chi-restraints excluded: chain A residue 507 GLN Chi-restraints excluded: chain A residue 615 ASP Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain B residue 371 ARG Chi-restraints excluded: chain B residue 602 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.0980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 66 optimal weight: 0.0980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 605 ASN A 712 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.126505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099569 restraints weight = 8450.351| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.98 r_work: 0.3139 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3555 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= 0.185 Angle : 0.541 10.092 9770 Z= 0.268 Chirality : 0.041 0.160 1014 Planarity : 0.004 0.043 1240 Dihedral : 10.267 91.965 962 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.20 % Allowed : 14.49 % Favored : 84.31 % 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: 1.22 (0.29), residues: 834 helix: 1.42 (0.30), residues: 314 sheet: 0.34 (0.54), residues: 96 loop : 0.62 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 587 HIS 0.009 0.001 HIS B 714 PHE 0.047 0.001 PHE B 355 TYR 0.010 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: 2962.25 seconds wall clock time: 54 minutes 31.93 seconds (3271.93 seconds total)