Starting phenix.real_space_refine on Thu Nov 14 19:56:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1k_40970/11_2024/8t1k_40970.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1k_40970/11_2024/8t1k_40970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1k_40970/11_2024/8t1k_40970.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1k_40970/11_2024/8t1k_40970.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1k_40970/11_2024/8t1k_40970.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t1k_40970/11_2024/8t1k_40970.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.141 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 Zn 1 6.06 5 S 42 5.16 5 C 4460 2.51 5 N 1202 2.21 5 O 1266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 6973 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3414 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 396} Chain: "B" Number of atoms: 3414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3414 Classifications: {'peptide': 419} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 396} Chain: "A" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {' ZN': 1, 'H4B': 1, 'HEM': 1} Inner-chain residues flagged as termini: ['pdbres="ARG A1502 "'] Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 60 Unusual residues: {'H4B': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 234 SG CYS A 326 36.136 27.320 47.401 1.00 0.00 S ATOM 274 SG CYS A 331 36.502 30.069 50.826 1.00 0.00 S ATOM 3648 SG CYS B 326 33.713 27.338 51.424 1.00 0.00 S ATOM 3688 SG CYS B 331 33.825 30.349 48.205 1.00 0.00 S ATOM 965 SG CYS A 415 29.189 41.684 34.489 1.00 0.00 S ATOM 4379 SG CYS B 415 43.340 39.579 64.879 1.00 0.00 S Time building chain proxies: 5.27, per 1000 atoms: 0.76 Number of scatterers: 6973 At special positions: 0 Unit cell: (74.784, 82.992, 101.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Fe 2 26.01 S 42 16.00 O 1266 8.00 N 1202 7.00 C 4460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.80 Conformation dependent library (CDL) restraints added in 934.2 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1501 " pdb="ZN ZN A1501 " - pdb=" SG CYS B 331 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 326 " pdb="ZN ZN A1501 " - pdb=" SG CYS A 331 " pdb="ZN ZN A1501 " - pdb=" SG CYS B 326 " Number of angles added : 6 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1584 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 16 sheets defined 44.8% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 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 508 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 removed outlier: 3.586A pdb=" N THR A 655 " --> pdb=" O HIS A 651 " (cutoff:3.500A) 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: 3.647A 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 692 Proline residue: B 689 - end of helix removed outlier: 3.614A pdb=" N HIS B 692 " --> pdb=" O PRO B 689 " (cutoff:3.500A) 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: 6.499A 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: 6.190A pdb=" N TYR B 588 " --> pdb=" O VAL B 649 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 295 hydrogen bonds defined for protein. 738 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: 2.04 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.35: 2195 1.35 - 1.55: 4911 1.55 - 1.76: 4 1.76 - 1.96: 65 1.96 - 2.17: 5 Bond restraints: 7180 Sorted by residual: bond pdb=" C TYR B 588 " pdb=" O TYR B 588 " ideal model delta sigma weight residual 1.235 1.141 0.094 1.18e-02 7.18e+03 6.35e+01 bond pdb=" CA TYR B 588 " pdb=" C TYR B 588 " ideal model delta sigma weight residual 1.523 1.424 0.099 1.24e-02 6.50e+03 6.31e+01 bond pdb=" C3B HEM B1503 " pdb=" CAB HEM B1503 " ideal model delta sigma weight residual 1.544 1.393 0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" C3B HEM A1504 " pdb=" CAB HEM A1504 " ideal model delta sigma weight residual 1.544 1.394 0.150 2.00e-02 2.50e+03 5.60e+01 bond pdb=" C3C HEM B1503 " pdb=" CAC HEM B1503 " ideal model delta sigma weight residual 1.544 1.402 0.142 2.00e-02 2.50e+03 5.07e+01 ... (remaining 7175 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.39: 9683 5.39 - 10.77: 83 10.77 - 16.16: 2 16.16 - 21.55: 0 21.55 - 26.93: 2 Bond angle restraints: 9770 Sorted by residual: angle pdb=" CA TYR B 588 " pdb=" C TYR B 588 " pdb=" O TYR B 588 " ideal model delta sigma weight residual 120.80 111.77 9.03 1.11e+00 8.12e-01 6.62e+01 angle pdb=" N LEU B 354 " pdb=" CA LEU B 354 " pdb=" C LEU B 354 " ideal model delta sigma weight residual 111.36 119.12 -7.76 1.09e+00 8.42e-01 5.07e+01 angle pdb=" N LEU A 354 " pdb=" CA LEU A 354 " pdb=" C LEU A 354 " ideal model delta sigma weight residual 111.36 119.06 -7.70 1.09e+00 8.42e-01 4.99e+01 angle pdb=" N ASN A 712 " pdb=" CA ASN A 712 " pdb=" C ASN A 712 " ideal model delta sigma weight residual 113.17 105.57 7.60 1.26e+00 6.30e-01 3.64e+01 angle pdb=" N ASN B 712 " pdb=" CA ASN B 712 " pdb=" C ASN B 712 " ideal model delta sigma weight residual 113.17 105.62 7.55 1.26e+00 6.30e-01 3.59e+01 ... (remaining 9765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.63: 4086 21.63 - 43.27: 99 43.27 - 64.90: 26 64.90 - 86.54: 11 86.54 - 108.17: 8 Dihedral angle restraints: 4230 sinusoidal: 1778 harmonic: 2452 Sorted by residual: dihedral pdb=" C2B HEM A1504 " pdb=" C3B HEM A1504 " pdb=" CAB HEM A1504 " pdb=" CBB HEM A1504 " ideal model delta sinusoidal sigma weight residual -180.00 -106.49 -73.51 2 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" C2B HEM B1503 " pdb=" C3B HEM B1503 " pdb=" CAB HEM B1503 " pdb=" CBB HEM B1503 " ideal model delta sinusoidal sigma weight residual -180.00 -117.70 -62.30 2 1.00e+01 1.00e-02 3.76e+01 dihedral pdb=" CA TYR A 588 " pdb=" C TYR A 588 " pdb=" N MET A 589 " pdb=" CA MET A 589 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 4227 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 709 0.076 - 0.152: 258 0.152 - 0.228: 40 0.228 - 0.304: 5 0.304 - 0.380: 2 Chirality restraints: 1014 Sorted by residual: chirality pdb=" CA ASP A 471 " pdb=" N ASP A 471 " pdb=" C ASP A 471 " pdb=" CB ASP A 471 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CA VAL A 474 " pdb=" N VAL A 474 " pdb=" C VAL A 474 " pdb=" CB VAL A 474 " both_signs ideal model delta sigma weight residual False 2.44 2.79 -0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA ASP B 471 " pdb=" N ASP B 471 " pdb=" C ASP B 471 " pdb=" CB ASP B 471 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.10e+00 ... (remaining 1011 not shown) Planarity restraints: 1240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1A HEM A1504 " -0.016 2.00e-02 2.50e+03 1.26e-01 3.55e+02 pdb=" C2A HEM A1504 " -0.038 2.00e-02 2.50e+03 pdb=" C3A HEM A1504 " -0.104 2.00e-02 2.50e+03 pdb=" C4A HEM A1504 " -0.015 2.00e-02 2.50e+03 pdb=" CAA HEM A1504 " 0.251 2.00e-02 2.50e+03 pdb=" CHA HEM A1504 " -0.100 2.00e-02 2.50e+03 pdb=" CHB HEM A1504 " 0.173 2.00e-02 2.50e+03 pdb=" CMA HEM A1504 " -0.161 2.00e-02 2.50e+03 pdb=" NA HEM A1504 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND HEM B1503 " -0.137 2.00e-02 2.50e+03 1.08e-01 2.62e+02 pdb=" C1D HEM B1503 " -0.147 2.00e-02 2.50e+03 pdb=" C2D HEM B1503 " -0.080 2.00e-02 2.50e+03 pdb=" C3D HEM B1503 " -0.024 2.00e-02 2.50e+03 pdb=" C4D HEM B1503 " -0.002 2.00e-02 2.50e+03 pdb=" CAD HEM B1503 " -0.003 2.00e-02 2.50e+03 pdb=" CHA HEM B1503 " 0.145 2.00e-02 2.50e+03 pdb=" CHD HEM B1503 " 0.179 2.00e-02 2.50e+03 pdb=" CMD HEM B1503 " 0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB HEM A1504 " -0.164 2.00e-02 2.50e+03 1.01e-01 2.27e+02 pdb=" C1B HEM A1504 " -0.019 2.00e-02 2.50e+03 pdb=" C2B HEM A1504 " 0.013 2.00e-02 2.50e+03 pdb=" C3B HEM A1504 " 0.002 2.00e-02 2.50e+03 pdb=" C4B HEM A1504 " -0.071 2.00e-02 2.50e+03 pdb=" CAB HEM A1504 " 0.092 2.00e-02 2.50e+03 pdb=" CHB HEM A1504 " 0.181 2.00e-02 2.50e+03 pdb=" CHC HEM A1504 " 0.073 2.00e-02 2.50e+03 pdb=" CMB HEM A1504 " -0.108 2.00e-02 2.50e+03 ... (remaining 1237 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 2278 2.86 - 3.37: 6431 3.37 - 3.88: 11891 3.88 - 4.39: 14786 4.39 - 4.90: 23441 Nonbonded interactions: 58827 Sorted by model distance: nonbonded pdb=" N TYR B 588 " pdb=" O TYR B 588 " model vdw 2.350 2.496 nonbonded pdb=" NZ LYS B 359 " pdb=" OD2 ASP B 363 " model vdw 2.434 3.120 nonbonded pdb=" OE1 GLN B 478 " pdb=" NH1 ARG B 481 " model vdw 2.469 3.120 nonbonded pdb=" O THR A 433 " pdb=" ND2 ASN A 527 " model vdw 2.493 3.120 nonbonded pdb=" N ASN B 712 " pdb=" N THR B 713 " model vdw 2.502 2.560 ... (remaining 58822 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: 2.280 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 21.710 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.154 7180 Z= 0.766 Angle : 1.456 26.935 9770 Z= 0.978 Chirality : 0.074 0.380 1014 Planarity : 0.009 0.126 1240 Dihedral : 12.821 108.170 2646 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 834 helix: -0.17 (0.26), residues: 296 sheet: 0.10 (0.54), residues: 76 loop : 0.34 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.006 TRP A 676 HIS 0.004 0.000 HIS B 470 PHE 0.035 0.003 PHE B 554 TYR 0.100 0.014 TYR B 604 ARG 0.008 0.001 ARG A 414 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.807 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2553 time to fit residues: 44.4698 Evaluate side-chains 80 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.736 ------------------------------------------------------------------------------- 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: 0.5980 chunk 62 optimal weight: 0.0040 chunk 34 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN A 507 GLN A 642 GLN B 454 ASN B 487 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2221 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= 0.217 Angle : 0.614 16.778 9770 Z= 0.301 Chirality : 0.043 0.134 1014 Planarity : 0.004 0.035 1240 Dihedral : 11.310 96.445 962 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.20 % Allowed : 6.12 % Favored : 92.69 % 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: 1.32 (0.28), residues: 834 helix: 1.58 (0.31), residues: 298 sheet: 0.00 (0.58), residues: 76 loop : 0.71 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 625 HIS 0.004 0.001 HIS A 714 PHE 0.018 0.002 PHE A 355 TYR 0.012 0.001 TYR B 366 ARG 0.005 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.781 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 87 average time/residue: 0.2431 time to fit residues: 27.1956 Evaluate side-chains 72 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 701 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.0020 chunk 23 optimal weight: 0.0570 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 59 optimal weight: 0.0040 overall best weight: 0.2918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 507 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2617 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= 0.164 Angle : 0.517 11.685 9770 Z= 0.257 Chirality : 0.041 0.133 1014 Planarity : 0.004 0.035 1240 Dihedral : 10.248 89.905 962 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.93 % Allowed : 7.18 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.29), residues: 834 helix: 1.83 (0.31), residues: 298 sheet: 0.44 (0.53), residues: 98 loop : 0.65 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 587 HIS 0.004 0.001 HIS A 445 PHE 0.016 0.001 PHE A 355 TYR 0.010 0.001 TYR B 366 ARG 0.004 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.860 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 79 average time/residue: 0.2384 time to fit residues: 24.5530 Evaluate side-chains 72 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 701 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 79 optimal weight: 0.0970 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7180 Z= 0.245 Angle : 0.578 15.690 9770 Z= 0.272 Chirality : 0.043 0.142 1014 Planarity : 0.004 0.036 1240 Dihedral : 10.461 92.260 962 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.33 % Allowed : 7.05 % Favored : 91.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.29), residues: 834 helix: 1.65 (0.31), residues: 298 sheet: 0.13 (0.52), residues: 96 loop : 0.54 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 587 HIS 0.005 0.001 HIS B 651 PHE 0.014 0.002 PHE B 355 TYR 0.011 0.001 TYR B 366 ARG 0.003 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.747 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 78 average time/residue: 0.2653 time to fit residues: 26.6208 Evaluate side-chains 77 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 701 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 0.4980 chunk 32 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 71 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 7180 Z= 0.263 Angle : 0.583 14.899 9770 Z= 0.274 Chirality : 0.043 0.139 1014 Planarity : 0.004 0.037 1240 Dihedral : 10.774 96.461 962 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.13 % Allowed : 7.31 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.29), residues: 834 helix: 1.52 (0.30), residues: 298 sheet: -0.06 (0.52), residues: 96 loop : 0.45 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 587 HIS 0.005 0.001 HIS B 651 PHE 0.013 0.002 PHE A 355 TYR 0.009 0.001 TYR A 366 ARG 0.004 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.818 Fit side-chains REVERT: A 328 GLU cc_start: 0.7482 (mp0) cc_final: 0.7250 (mp0) REVERT: B 398 ASP cc_start: 0.6729 (m-30) cc_final: 0.6514 (m-30) outliers start: 16 outliers final: 12 residues processed: 77 average time/residue: 0.2464 time to fit residues: 24.5474 Evaluate side-chains 79 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 SER Chi-restraints excluded: chain B residue 539 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 15 optimal weight: 0.0470 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 79 optimal weight: 0.0060 chunk 65 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 0.5094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS A 478 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7180 Z= 0.202 Angle : 0.531 11.762 9770 Z= 0.256 Chirality : 0.042 0.163 1014 Planarity : 0.004 0.038 1240 Dihedral : 10.254 91.652 962 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.46 % Allowed : 8.51 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.29), residues: 834 helix: 1.55 (0.30), residues: 298 sheet: -0.08 (0.52), residues: 96 loop : 0.47 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 587 HIS 0.004 0.001 HIS B 651 PHE 0.013 0.001 PHE A 355 TYR 0.009 0.001 TYR A 366 ARG 0.004 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.745 Fit side-chains REVERT: A 332 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7820 (mtm) REVERT: B 398 ASP cc_start: 0.6803 (m-30) cc_final: 0.6582 (m-30) outliers start: 11 outliers final: 9 residues processed: 75 average time/residue: 0.2387 time to fit residues: 23.1539 Evaluate side-chains 79 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 0.0020 chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7180 Z= 0.236 Angle : 0.563 13.566 9770 Z= 0.267 Chirality : 0.043 0.167 1014 Planarity : 0.004 0.038 1240 Dihedral : 10.324 94.532 962 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.73 % Allowed : 8.78 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.29), residues: 834 helix: 1.50 (0.30), residues: 298 sheet: -0.17 (0.52), residues: 96 loop : 0.44 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 587 HIS 0.005 0.001 HIS B 651 PHE 0.013 0.002 PHE A 355 TYR 0.009 0.001 TYR A 366 ARG 0.004 0.000 ARG B 699 *********************** 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 83 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.823 Fit side-chains REVERT: A 332 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7812 (mtm) REVERT: A 550 LYS cc_start: 0.8018 (mmtt) cc_final: 0.7772 (mmtp) REVERT: B 398 ASP cc_start: 0.6811 (m-30) cc_final: 0.6585 (m-30) outliers start: 13 outliers final: 11 residues processed: 77 average time/residue: 0.2551 time to fit residues: 25.3378 Evaluate side-chains 78 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 66 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 62 optimal weight: 0.0370 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7180 Z= 0.206 Angle : 0.536 11.388 9770 Z= 0.259 Chirality : 0.042 0.178 1014 Planarity : 0.004 0.038 1240 Dihedral : 9.966 92.230 962 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.86 % Allowed : 9.18 % Favored : 88.96 % 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: 1.02 (0.29), residues: 834 helix: 1.42 (0.31), residues: 302 sheet: -0.14 (0.53), residues: 96 loop : 0.48 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 587 HIS 0.004 0.001 HIS B 651 PHE 0.013 0.001 PHE A 355 TYR 0.009 0.001 TYR B 366 ARG 0.004 0.000 ARG B 699 *********************** 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 81 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.945 Fit side-chains REVERT: A 332 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7780 (mtm) REVERT: A 550 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7808 (mmtp) REVERT: B 398 ASP cc_start: 0.6777 (m-30) cc_final: 0.6525 (m-30) outliers start: 14 outliers final: 12 residues processed: 74 average time/residue: 0.2785 time to fit residues: 26.7240 Evaluate side-chains 78 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 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 470 HIS A 527 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7180 Z= 0.269 Angle : 0.586 14.642 9770 Z= 0.276 Chirality : 0.044 0.170 1014 Planarity : 0.004 0.037 1240 Dihedral : 10.363 96.898 962 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.86 % Allowed : 9.18 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.29), residues: 834 helix: 1.34 (0.31), residues: 302 sheet: -0.23 (0.52), residues: 96 loop : 0.43 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 587 HIS 0.006 0.001 HIS B 651 PHE 0.014 0.002 PHE A 355 TYR 0.009 0.001 TYR A 366 ARG 0.005 0.000 ARG B 667 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.707 Fit side-chains REVERT: A 332 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.7794 (mtm) REVERT: A 550 LYS cc_start: 0.8066 (mmtt) cc_final: 0.7800 (mmtp) REVERT: B 398 ASP cc_start: 0.6806 (m-30) cc_final: 0.6550 (m-30) outliers start: 14 outliers final: 13 residues processed: 73 average time/residue: 0.2284 time to fit residues: 21.5496 Evaluate side-chains 77 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 622 SER Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 75 optimal weight: 0.5980 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 0.1980 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 470 HIS A 527 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7180 Z= 0.219 Angle : 0.558 12.681 9770 Z= 0.267 Chirality : 0.043 0.174 1014 Planarity : 0.004 0.038 1240 Dihedral : 10.216 95.588 962 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.86 % Allowed : 9.44 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.29), residues: 834 helix: 1.35 (0.30), residues: 302 sheet: -0.23 (0.52), residues: 96 loop : 0.45 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 587 HIS 0.005 0.001 HIS B 651 PHE 0.013 0.001 PHE A 355 TYR 0.008 0.001 TYR A 366 ARG 0.005 0.000 ARG B 667 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.810 Fit side-chains REVERT: A 332 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7793 (mtm) REVERT: A 550 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7800 (mmtp) REVERT: B 398 ASP cc_start: 0.6783 (m-30) cc_final: 0.6532 (m-30) outliers start: 14 outliers final: 13 residues processed: 73 average time/residue: 0.2666 time to fit residues: 25.3119 Evaluate side-chains 77 residues out of total 752 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 527 ASN Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain A residue 621 THR Chi-restraints excluded: chain A residue 649 VAL Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 477 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 65 optimal weight: 0.5980 chunk 27 optimal weight: 0.0970 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.107383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.084652 restraints weight = 7819.019| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 1.51 r_work: 0.2653 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2515 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 7180 Z= 0.244 Angle : 0.942 59.181 9770 Z= 0.529 Chirality : 0.044 0.330 1014 Planarity : 0.004 0.071 1240 Dihedral : 10.223 95.559 962 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.60 % Allowed : 9.44 % Favored : 88.96 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.29), residues: 834 helix: 1.35 (0.30), residues: 302 sheet: -0.23 (0.52), residues: 96 loop : 0.44 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 587 HIS 0.004 0.001 HIS B 651 PHE 0.013 0.001 PHE A 355 TYR 0.008 0.001 TYR A 366 ARG 0.003 0.000 ARG B 667 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1781.90 seconds wall clock time: 41 minutes 18.48 seconds (2478.48 seconds total)