Starting phenix.real_space_refine on Wed Mar 12 23:26:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xmt_22263/03_2025/6xmt_22263.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xmt_22263/03_2025/6xmt_22263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xmt_22263/03_2025/6xmt_22263.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xmt_22263/03_2025/6xmt_22263.map" model { file = "/net/cci-nas-00/data/ceres_data/6xmt_22263/03_2025/6xmt_22263.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xmt_22263/03_2025/6xmt_22263.cif" } resolution = 3.3 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= 0.057 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 38 5.16 5 Be 1 3.05 5 C 5370 2.51 5 N 1374 2.21 5 O 1537 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8324 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8319 Classifications: {'peptide': 1092} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 49, 'TRANS': 1042} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 260 Unresolved non-hydrogen angles: 327 Unresolved non-hydrogen dihedrals: 221 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 164 Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.76, per 1000 atoms: 0.69 Number of scatterers: 8324 At special positions: 0 Unit cell: (91.63, 88.06, 145.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 38 16.00 Mg 1 11.99 F 3 9.00 O 1537 8.00 N 1374 7.00 C 5370 6.00 Be 1 4.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.0 seconds 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 46.5% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 28 through 44 removed outlier: 3.804A pdb=" N PHE A 32 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Proline residue: A 34 - end of helix Processing helix chain 'A' and resid 57 through 74 removed outlier: 3.540A pdb=" N LEU A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 78 through 86 Processing helix chain 'A' and resid 156 through 162 removed outlier: 3.866A pdb=" N PHE A 160 " --> pdb=" O LYS A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 199 through 214 Processing helix chain 'A' and resid 218 through 247 removed outlier: 3.697A pdb=" N MET A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 336 removed outlier: 4.409A pdb=" N ILE A 336 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 375 removed outlier: 3.703A pdb=" N GLU A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 372 through 375' Processing helix chain 'A' and resid 376 through 388 Processing helix chain 'A' and resid 396 through 425 Processing helix chain 'A' and resid 427 through 441 removed outlier: 3.627A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 463 Processing helix chain 'A' and resid 471 through 480 removed outlier: 3.686A pdb=" N ILE A 475 " --> pdb=" O PRO A 472 " (cutoff:3.500A) Proline residue: A 476 - end of helix removed outlier: 3.507A pdb=" N GLY A 479 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG A 480 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 removed outlier: 3.791A pdb=" N GLY A 530 " --> pdb=" O ILE A 526 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 557 Processing helix chain 'A' and resid 606 through 612 removed outlier: 3.777A pdb=" N GLU A 612 " --> pdb=" O GLU A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 655 through 660 removed outlier: 4.318A pdb=" N VAL A 659 " --> pdb=" O ASN A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 688 Processing helix chain 'A' and resid 700 through 712 Processing helix chain 'A' and resid 753 through 758 Processing helix chain 'A' and resid 766 through 772 Processing helix chain 'A' and resid 778 through 784 Processing helix chain 'A' and resid 795 through 808 removed outlier: 3.940A pdb=" N PHE A 799 " --> pdb=" O SER A 795 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 827 Processing helix chain 'A' and resid 837 through 854 Processing helix chain 'A' and resid 972 through 1010 removed outlier: 3.667A pdb=" N CYS A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1018 through 1035 Processing helix chain 'A' and resid 1055 through 1084 Processing helix chain 'A' and resid 1099 through 1119 removed outlier: 3.903A pdb=" N THR A1103 " --> pdb=" O SER A1099 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A1108 " --> pdb=" O GLY A1104 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A1117 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1152 removed outlier: 3.742A pdb=" N THR A1152 " --> pdb=" O LEU A1148 " (cutoff:3.500A) Processing helix chain 'A' and resid 1155 through 1162 Processing helix chain 'A' and resid 1169 through 1197 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.726A pdb=" N TYR A 102 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER A 15 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A 100 " --> pdb=" O SER A 15 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N LEU A 17 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N HIS A 98 " --> pdb=" O LEU A 17 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A 111 " --> pdb=" O ILE A 101 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'A' and resid 127 through 130 removed outlier: 3.586A pdb=" N PHE A 128 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 263 through 267 removed outlier: 4.862A pdb=" N ASN A 257 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 279 " --> pdb=" O ASN A 257 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LEU A 277 " --> pdb=" O PHE A 259 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ASP A 292 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 314 through 316 removed outlier: 6.850A pdb=" N SER A 299 " --> pdb=" O VAL A 348 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N VAL A 348 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 301 " --> pdb=" O LEU A 346 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS A 344 " --> pdb=" O ASN A 303 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 467 through 469 removed outlier: 6.480A pdb=" N GLY A 830 " --> pdb=" O PHE A 964 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N SER A 966 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA A 832 " --> pdb=" O SER A 966 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET A 813 " --> pdb=" O ILE A 831 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N LEU A 833 " --> pdb=" O MET A 813 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY A 815 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 8.372A pdb=" N CYS A 814 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N CYS A 485 " --> pdb=" O CYS A 814 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N CYS A 484 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N ILE A 696 " --> pdb=" O CYS A 484 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N PHE A 486 " --> pdb=" O ILE A 696 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER A 693 " --> pdb=" O TRP A 787 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N TYR A 789 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N MET A 695 " --> pdb=" O TYR A 789 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE A 763 " --> pdb=" O THR A 786 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL A 788 " --> pdb=" O ILE A 763 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 719 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP A 722 " --> pdb=" O LEU A 733 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 498 through 501 removed outlier: 3.662A pdb=" N VAL A 498 " --> pdb=" O HIS A 672 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ILE A 670 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE A 671 " --> pdb=" O ARG A 634 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 536 through 537 removed outlier: 3.595A pdb=" N VAL A 536 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 559 through 560 removed outlier: 3.613A pdb=" N ALA A 559 " --> pdb=" O TYR A 567 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 575 through 579 removed outlier: 6.760A pdb=" N ILE A 592 " --> pdb=" O ILE A 577 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 667 " --> pdb=" O LEU A 638 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER A 640 " --> pdb=" O PHE A 665 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE A 665 " --> pdb=" O SER A 640 " (cutoff:3.500A) 402 hydrogen bonds defined for protein. 1167 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: 3.48 Time building geometry restraints manager: 2.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2200 1.33 - 1.45: 1399 1.45 - 1.57: 4832 1.57 - 1.69: 0 1.69 - 1.81: 63 Bond restraints: 8494 Sorted by residual: bond pdb=" F2 BEF A1301 " pdb="BE BEF A1301 " ideal model delta sigma weight residual 1.476 1.560 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" F3 BEF A1301 " pdb="BE BEF A1301 " ideal model delta sigma weight residual 1.476 1.545 -0.069 2.00e-02 2.50e+03 1.17e+01 bond pdb=" F1 BEF A1301 " pdb="BE BEF A1301 " ideal model delta sigma weight residual 1.476 1.534 -0.058 2.00e-02 2.50e+03 8.32e+00 bond pdb=" N VAL A 29 " pdb=" CA VAL A 29 " ideal model delta sigma weight residual 1.460 1.483 -0.023 1.19e-02 7.06e+03 3.79e+00 bond pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 1.524 1.548 -0.024 1.23e-02 6.61e+03 3.68e+00 ... (remaining 8489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 11421 2.54 - 5.07: 99 5.07 - 7.61: 7 7.61 - 10.15: 2 10.15 - 12.69: 1 Bond angle restraints: 11530 Sorted by residual: angle pdb=" N VAL A 29 " pdb=" CA VAL A 29 " pdb=" C VAL A 29 " ideal model delta sigma weight residual 110.53 117.37 -6.84 9.40e-01 1.13e+00 5.30e+01 angle pdb=" C LEU A 30 " pdb=" N PRO A 31 " pdb=" CA PRO A 31 " ideal model delta sigma weight residual 119.05 125.60 -6.55 1.11e+00 8.12e-01 3.48e+01 angle pdb=" N PRO A 34 " pdb=" CA PRO A 34 " pdb=" CB PRO A 34 " ideal model delta sigma weight residual 103.33 109.78 -6.45 1.10e+00 8.26e-01 3.44e+01 angle pdb=" F2 BEF A1301 " pdb="BE BEF A1301 " pdb=" F3 BEF A1301 " ideal model delta sigma weight residual 119.96 107.27 12.69 3.00e+00 1.11e-01 1.79e+01 angle pdb=" N VAL A 198 " pdb=" CA VAL A 198 " pdb=" C VAL A 198 " ideal model delta sigma weight residual 113.42 108.96 4.46 1.17e+00 7.31e-01 1.45e+01 ... (remaining 11525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 4658 17.44 - 34.87: 370 34.87 - 52.31: 50 52.31 - 69.74: 6 69.74 - 87.18: 4 Dihedral angle restraints: 5088 sinusoidal: 1922 harmonic: 3166 Sorted by residual: dihedral pdb=" N PRO A 34 " pdb=" C PRO A 34 " pdb=" CA PRO A 34 " pdb=" CB PRO A 34 " ideal model delta harmonic sigma weight residual 115.10 123.28 -8.18 0 2.50e+00 1.60e-01 1.07e+01 dihedral pdb=" CB GLU A 420 " pdb=" CG GLU A 420 " pdb=" CD GLU A 420 " pdb=" OE1 GLU A 420 " ideal model delta sinusoidal sigma weight residual 0.00 -87.18 87.18 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CA TYR A 516 " pdb=" C TYR A 516 " pdb=" N SER A 517 " pdb=" CA SER A 517 " ideal model delta harmonic sigma weight residual -180.00 -164.24 -15.76 0 5.00e+00 4.00e-02 9.94e+00 ... (remaining 5085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1104 0.052 - 0.104: 219 0.104 - 0.156: 28 0.156 - 0.208: 1 0.208 - 0.260: 1 Chirality restraints: 1353 Sorted by residual: chirality pdb=" CA PRO A 34 " pdb=" N PRO A 34 " pdb=" C PRO A 34 " pdb=" CB PRO A 34 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CG LEU A 73 " pdb=" CB LEU A 73 " pdb=" CD1 LEU A 73 " pdb=" CD2 LEU A 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CG LEU A 70 " pdb=" CB LEU A 70 " pdb=" CD1 LEU A 70 " pdb=" CD2 LEU A 70 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.15 2.00e-01 2.50e+01 6.01e-01 ... (remaining 1350 not shown) Planarity restraints: 1464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 74 " 0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 75 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 29 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.55e+00 pdb=" C VAL A 29 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 29 " -0.010 2.00e-02 2.50e+03 pdb=" N LEU A 30 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 273 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO A 274 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " 0.022 5.00e-02 4.00e+02 ... (remaining 1461 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 28 2.43 - 3.05: 5188 3.05 - 3.67: 11571 3.67 - 4.28: 16319 4.28 - 4.90: 28499 Nonbonded interactions: 61605 Sorted by model distance: nonbonded pdb=" F1 BEF A1301 " pdb="MG MG A1302 " model vdw 1.814 2.120 nonbonded pdb=" OD2 ASP A 487 " pdb=" F1 BEF A1301 " model vdw 1.884 2.990 nonbonded pdb=" OD1 ASN A 987 " pdb=" NH1 ARG A1127 " model vdw 2.249 3.120 nonbonded pdb=" O THR A 489 " pdb="MG MG A1302 " model vdw 2.275 2.170 nonbonded pdb=" OG1 THR A 751 " pdb=" OE1 GLN A 778 " model vdw 2.276 3.040 ... (remaining 61600 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.220 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: 0.380 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.020 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 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 : 0.004 0.084 8494 Z= 0.246 Angle : 0.606 12.687 11530 Z= 0.347 Chirality : 0.042 0.260 1353 Planarity : 0.004 0.041 1464 Dihedral : 12.442 87.180 3036 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.38 (0.23), residues: 1082 helix: -0.21 (0.22), residues: 490 sheet: -2.82 (0.38), residues: 131 loop : -2.73 (0.24), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1187 HIS 0.005 0.001 HIS A 672 PHE 0.014 0.001 PHE A 405 TYR 0.014 0.001 TYR A1057 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.968 Fit side-chains REVERT: A 695 MET cc_start: 0.8688 (ttm) cc_final: 0.8380 (ttm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1699 time to fit residues: 14.7107 Evaluate side-chains 35 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 55 optimal weight: 0.0670 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.4980 chunk 98 optimal weight: 0.8980 overall best weight: 0.8520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 166 HIS A 196 HIS A1050 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.080818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.060415 restraints weight = 23648.686| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.36 r_work: 0.2962 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8494 Z= 0.169 Angle : 0.520 8.505 11530 Z= 0.267 Chirality : 0.040 0.152 1353 Planarity : 0.004 0.041 1464 Dihedral : 4.066 16.099 1149 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.46 % Allowed : 8.87 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.25), residues: 1082 helix: 1.04 (0.24), residues: 490 sheet: -2.61 (0.37), residues: 145 loop : -2.10 (0.26), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1187 HIS 0.008 0.001 HIS A 672 PHE 0.014 0.001 PHE A 226 TYR 0.010 0.001 TYR A1057 ARG 0.004 0.000 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.998 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 43 average time/residue: 0.1543 time to fit residues: 11.0891 Evaluate side-chains 40 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 64 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 44 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.078893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.058350 restraints weight = 24406.743| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.40 r_work: 0.2918 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 8494 Z= 0.266 Angle : 0.537 7.613 11530 Z= 0.275 Chirality : 0.041 0.145 1353 Planarity : 0.003 0.040 1464 Dihedral : 4.145 15.899 1149 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.48 % Allowed : 11.38 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.51 (0.26), residues: 1082 helix: 1.55 (0.24), residues: 493 sheet: -2.39 (0.38), residues: 147 loop : -1.81 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1187 HIS 0.008 0.001 HIS A 672 PHE 0.017 0.001 PHE A 226 TYR 0.011 0.001 TYR A1057 ARG 0.003 0.000 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.918 Fit side-chains REVERT: A 813 MET cc_start: 0.9046 (tpt) cc_final: 0.8736 (tpt) outliers start: 13 outliers final: 7 residues processed: 50 average time/residue: 0.1410 time to fit residues: 11.7643 Evaluate side-chains 43 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 86 optimal weight: 3.9990 chunk 92 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 ASN A 129 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.078817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.058334 restraints weight = 23927.111| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.38 r_work: 0.2913 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8494 Z= 0.247 Angle : 0.531 9.247 11530 Z= 0.269 Chirality : 0.040 0.151 1353 Planarity : 0.003 0.040 1464 Dihedral : 4.132 16.162 1149 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.48 % Allowed : 12.97 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.18 (0.26), residues: 1082 helix: 1.80 (0.24), residues: 493 sheet: -2.16 (0.39), residues: 142 loop : -1.65 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1187 HIS 0.007 0.001 HIS A 672 PHE 0.018 0.001 PHE A 226 TYR 0.010 0.001 TYR A1057 ARG 0.002 0.000 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 36 time to evaluate : 1.005 Fit side-chains REVERT: A 813 MET cc_start: 0.9046 (tpt) cc_final: 0.8772 (tpt) outliers start: 13 outliers final: 11 residues processed: 46 average time/residue: 0.1525 time to fit residues: 11.8470 Evaluate side-chains 46 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 14 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 0.2980 chunk 106 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1129 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.079824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.059139 restraints weight = 23866.867| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 3.44 r_work: 0.2935 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8494 Z= 0.165 Angle : 0.505 12.414 11530 Z= 0.251 Chirality : 0.039 0.153 1353 Planarity : 0.003 0.040 1464 Dihedral : 3.982 15.634 1149 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.93 % Allowed : 13.20 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.26), residues: 1082 helix: 1.98 (0.24), residues: 493 sheet: -1.96 (0.40), residues: 142 loop : -1.48 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1187 HIS 0.007 0.001 HIS A 672 PHE 0.018 0.001 PHE A 226 TYR 0.009 0.001 TYR A1057 ARG 0.002 0.000 ARG A1048 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.986 Fit side-chains REVERT: A 813 MET cc_start: 0.9049 (tpt) cc_final: 0.8750 (tpt) outliers start: 17 outliers final: 12 residues processed: 52 average time/residue: 0.1485 time to fit residues: 12.7282 Evaluate side-chains 47 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 4.9990 chunk 59 optimal weight: 0.0770 chunk 95 optimal weight: 0.7980 chunk 13 optimal weight: 0.0970 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 50.0000 chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 0.0000 overall best weight: 0.3740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 754 HIS A1129 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.081093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.061203 restraints weight = 23629.155| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.31 r_work: 0.2975 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 8494 Z= 0.131 Angle : 0.509 11.222 11530 Z= 0.250 Chirality : 0.039 0.152 1353 Planarity : 0.003 0.039 1464 Dihedral : 3.873 15.901 1149 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.71 % Allowed : 13.77 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.39 (0.26), residues: 1082 helix: 2.15 (0.24), residues: 493 sheet: -1.61 (0.41), residues: 144 loop : -1.29 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 787 HIS 0.005 0.000 HIS A 672 PHE 0.019 0.001 PHE A 226 TYR 0.007 0.001 TYR A1057 ARG 0.002 0.000 ARG A 426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 38 time to evaluate : 0.973 Fit side-chains REVERT: A 72 MET cc_start: 0.7926 (tmm) cc_final: 0.7193 (tpp) REVERT: A 813 MET cc_start: 0.9048 (tpt) cc_final: 0.8756 (tpt) outliers start: 15 outliers final: 11 residues processed: 50 average time/residue: 0.1492 time to fit residues: 12.5889 Evaluate side-chains 49 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 101 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 35 optimal weight: 0.4980 chunk 8 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 50 optimal weight: 0.1980 chunk 74 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.080922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.061077 restraints weight = 23725.227| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.32 r_work: 0.2974 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 8494 Z= 0.135 Angle : 0.495 10.613 11530 Z= 0.243 Chirality : 0.039 0.150 1353 Planarity : 0.003 0.038 1464 Dihedral : 3.786 15.332 1149 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.59 % Allowed : 13.99 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.59 (0.26), residues: 1082 helix: 2.32 (0.24), residues: 489 sheet: -1.41 (0.41), residues: 144 loop : -1.21 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 787 HIS 0.005 0.000 HIS A 672 PHE 0.019 0.001 PHE A 226 TYR 0.008 0.001 TYR A1057 ARG 0.002 0.000 ARG A 760 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 41 time to evaluate : 1.056 Fit side-chains REVERT: A 408 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8959 (mp) REVERT: A 813 MET cc_start: 0.9065 (tpt) cc_final: 0.8729 (tpt) outliers start: 14 outliers final: 12 residues processed: 53 average time/residue: 0.1444 time to fit residues: 12.9542 Evaluate side-chains 52 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.3980 chunk 103 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 3 optimal weight: 50.0000 chunk 24 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.080324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.059865 restraints weight = 24036.902| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 3.41 r_work: 0.2952 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8494 Z= 0.173 Angle : 0.499 10.349 11530 Z= 0.246 Chirality : 0.039 0.148 1353 Planarity : 0.003 0.038 1464 Dihedral : 3.809 15.970 1149 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.05 % Allowed : 14.11 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.66 (0.26), residues: 1082 helix: 2.36 (0.24), residues: 489 sheet: -1.31 (0.41), residues: 144 loop : -1.17 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 787 HIS 0.006 0.001 HIS A 672 PHE 0.019 0.001 PHE A 226 TYR 0.010 0.001 TYR A1057 ARG 0.001 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.951 Fit side-chains REVERT: A 72 MET cc_start: 0.7899 (tmm) cc_final: 0.7284 (tpp) REVERT: A 408 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8964 (mp) REVERT: A 813 MET cc_start: 0.9069 (tpt) cc_final: 0.8752 (tpt) outliers start: 18 outliers final: 15 residues processed: 55 average time/residue: 0.1474 time to fit residues: 13.5439 Evaluate side-chains 56 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 86 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 0 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.080378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.059804 restraints weight = 24036.956| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.46 r_work: 0.2948 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8494 Z= 0.159 Angle : 0.498 10.189 11530 Z= 0.244 Chirality : 0.039 0.148 1353 Planarity : 0.003 0.038 1464 Dihedral : 3.792 15.984 1149 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.71 % Allowed : 14.33 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.26), residues: 1082 helix: 2.44 (0.24), residues: 489 sheet: -1.17 (0.42), residues: 144 loop : -1.14 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 787 HIS 0.006 0.001 HIS A 672 PHE 0.020 0.001 PHE A 226 TYR 0.009 0.001 TYR A1057 ARG 0.001 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.934 Fit side-chains REVERT: A 72 MET cc_start: 0.7995 (tmm) cc_final: 0.7408 (tpp) REVERT: A 408 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8944 (mp) REVERT: A 813 MET cc_start: 0.9060 (tpt) cc_final: 0.8734 (tpt) outliers start: 15 outliers final: 14 residues processed: 53 average time/residue: 0.1468 time to fit residues: 12.8275 Evaluate side-chains 54 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 39 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 78 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.079957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.059960 restraints weight = 23822.942| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.33 r_work: 0.2941 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8494 Z= 0.196 Angle : 0.512 10.083 11530 Z= 0.253 Chirality : 0.039 0.149 1353 Planarity : 0.003 0.038 1464 Dihedral : 3.864 16.460 1149 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.93 % Allowed : 14.22 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1082 helix: 2.45 (0.24), residues: 489 sheet: -1.18 (0.42), residues: 144 loop : -1.14 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A1187 HIS 0.007 0.001 HIS A 672 PHE 0.021 0.001 PHE A 226 TYR 0.010 0.001 TYR A1057 ARG 0.002 0.000 ARG A 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2164 Ramachandran restraints generated. 1082 Oldfield, 0 Emsley, 1082 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.996 Fit side-chains REVERT: A 72 MET cc_start: 0.8080 (tmm) cc_final: 0.7605 (tpp) REVERT: A 408 ILE cc_start: 0.9175 (OUTLIER) cc_final: 0.8972 (mp) REVERT: A 813 MET cc_start: 0.9064 (tpt) cc_final: 0.8743 (tpt) outliers start: 17 outliers final: 15 residues processed: 53 average time/residue: 0.1475 time to fit residues: 12.9605 Evaluate side-chains 56 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 40 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 436 ILE Chi-restraints excluded: chain A residue 574 LEU Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 659 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1007 SER Chi-restraints excluded: chain A residue 1053 ILE Chi-restraints excluded: chain A residue 1111 VAL Chi-restraints excluded: chain A residue 1191 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 48 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 69 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 4 optimal weight: 30.0000 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 62 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1020 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.080098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.060132 restraints weight = 24012.855| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.34 r_work: 0.2944 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8494 Z= 0.179 Angle : 0.499 10.046 11530 Z= 0.247 Chirality : 0.039 0.148 1353 Planarity : 0.003 0.038 1464 Dihedral : 3.849 16.315 1149 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.05 % Allowed : 14.33 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.26), residues: 1082 helix: 2.48 (0.24), residues: 489 sheet: -1.10 (0.43), residues: 144 loop : -1.13 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1187 HIS 0.007 0.001 HIS A 672 PHE 0.021 0.001 PHE A 226 TYR 0.009 0.001 TYR A1057 ARG 0.001 0.000 ARG A 735 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3256.86 seconds wall clock time: 56 minutes 47.64 seconds (3407.64 seconds total)