Starting phenix.real_space_refine on Wed Aug 5 18:23:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z60_73829/08_2026/9z60_73829_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z60_73829/08_2026/9z60_73829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z60_73829/08_2026/9z60_73829_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z60_73829/08_2026/9z60_73829_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z60_73829/08_2026/9z60_73829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z60_73829/08_2026/9z60_73829.map" } resolution = 3.53 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.019 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: 5 Type Number sf(0) Gaussians S 27 5.16 5 C 3482 2.51 5 N 855 2.21 5 O 962 1.98 5 H 5396 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10722 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 7164 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 19, 'TRANS': 442} Chain breaks: 2 Chain: "B" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 1872 Classifications: {'peptide': 121} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain: "C" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 1658 Classifications: {'peptide': 111} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 103} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.50, per 1000 atoms: 0.14 Number of scatterers: 10722 At special positions: 0 Unit cell: (72.688, 79.296, 127.204, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 O 962 8.00 N 855 7.00 C 3482 6.00 H 5396 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS A 321 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 92 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 283.6 milliseconds 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1276 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 6 sheets defined 60.5% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 68 through 101 Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.604A pdb=" N GLU A 110 " --> pdb=" O ASP A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 115 Processing helix chain 'A' and resid 116 through 132 Processing helix chain 'A' and resid 133 through 147 Processing helix chain 'A' and resid 151 through 163 Proline residue: A 157 - end of helix removed outlier: 3.872A pdb=" N ASN A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 175 removed outlier: 4.271A pdb=" N THR A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 179 removed outlier: 4.445A pdb=" N GLY A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 179' Processing helix chain 'A' and resid 180 through 212 removed outlier: 4.406A pdb=" N HIS A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Proline residue: A 207 - end of helix Processing helix chain 'A' and resid 213 through 227 Processing helix chain 'A' and resid 235 through 250 removed outlier: 3.913A pdb=" N ASN A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Proline residue: A 244 - end of helix Processing helix chain 'A' and resid 253 through 259 Processing helix chain 'A' and resid 331 through 362 removed outlier: 3.583A pdb=" N CYS A 353 " --> pdb=" O THR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 376 removed outlier: 3.617A pdb=" N THR A 376 " --> pdb=" O LYS A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 402 Processing helix chain 'A' and resid 403 through 418 Proline residue: A 413 - end of helix Processing helix chain 'A' and resid 421 through 446 Proline residue: A 427 - end of helix removed outlier: 3.700A pdb=" N ALA A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 474 removed outlier: 4.325A pdb=" N GLY A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ASN A 454 " --> pdb=" O GLU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 479 Processing helix chain 'A' and resid 480 through 496 removed outlier: 3.822A pdb=" N ARG A 484 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 509 removed outlier: 4.021A pdb=" N ALA A 501 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 522 Processing helix chain 'A' and resid 522 through 550 Proline residue: A 532 - end of helix Processing helix chain 'A' and resid 556 through 564 removed outlier: 3.892A pdb=" N SER A 560 " --> pdb=" O ALA A 557 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TRP A 561 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASP A 562 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N PHE A 563 " --> pdb=" O SER A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 570 removed outlier: 3.525A pdb=" N HIS A 569 " --> pdb=" O PRO A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 583 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'C' and resid 83 through 87 removed outlier: 4.222A pdb=" N VAL C 87 " --> pdb=" O ALA C 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 5 through 6 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.438A pdb=" N GLU B 10 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N MET B 34 " --> pdb=" O TRP B 50 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TRP B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP B 36 " --> pdb=" O MET B 48 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 14 removed outlier: 6.625A pdb=" N MET C 37 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N TYR C 53 " --> pdb=" O MET C 37 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TRP C 39 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 14 removed outlier: 3.561A pdb=" N THR C 101 " --> pdb=" O GLN C 94 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 30 through 31 348 hydrogen bonds defined for protein. 981 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5390 1.03 - 1.23: 11 1.23 - 1.43: 2223 1.43 - 1.62: 3180 1.62 - 1.82: 42 Bond restraints: 10846 Sorted by residual: bond pdb=" N MET B 34 " pdb=" CA MET B 34 " ideal model delta sigma weight residual 1.457 1.492 -0.036 1.26e-02 6.30e+03 8.05e+00 bond pdb=" N ASN B 35 " pdb=" CA ASN B 35 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.93e+00 bond pdb=" N ASN B 99 " pdb=" CA ASN B 99 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.19e-02 7.06e+03 7.87e+00 bond pdb=" C20 CLR A 801 " pdb=" C22 CLR A 801 " ideal model delta sigma weight residual 1.535 1.588 -0.053 2.00e-02 2.50e+03 6.89e+00 bond pdb=" N ARG B 98 " pdb=" CA ARG B 98 " ideal model delta sigma weight residual 1.453 1.483 -0.030 1.31e-02 5.83e+03 5.34e+00 ... (remaining 10841 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 19356 1.58 - 3.16: 247 3.16 - 4.74: 29 4.74 - 6.32: 6 6.32 - 7.90: 2 Bond angle restraints: 19640 Sorted by residual: angle pdb=" CA ALA B 97 " pdb=" C ALA B 97 " pdb=" O ALA B 97 " ideal model delta sigma weight residual 120.32 116.08 4.24 1.10e+00 8.26e-01 1.48e+01 angle pdb=" CA ASN B 99 " pdb=" C ASN B 99 " pdb=" O ASN B 99 " ideal model delta sigma weight residual 121.16 117.22 3.94 1.13e+00 7.83e-01 1.22e+01 angle pdb=" CA ARG B 98 " pdb=" C ARG B 98 " pdb=" O ARG B 98 " ideal model delta sigma weight residual 121.94 117.95 3.99 1.15e+00 7.56e-01 1.20e+01 angle pdb=" CA ASN B 35 " pdb=" C ASN B 35 " pdb=" O ASN B 35 " ideal model delta sigma weight residual 120.71 117.30 3.41 1.06e+00 8.90e-01 1.03e+01 angle pdb=" N THR A 386 " pdb=" CA THR A 386 " pdb=" C THR A 386 " ideal model delta sigma weight residual 114.04 110.13 3.91 1.24e+00 6.50e-01 9.92e+00 ... (remaining 19635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4616 17.96 - 35.92: 373 35.92 - 53.88: 147 53.88 - 71.84: 31 71.84 - 89.80: 3 Dihedral angle restraints: 5170 sinusoidal: 2801 harmonic: 2369 Sorted by residual: dihedral pdb=" CB GLU B 57 " pdb=" CG GLU B 57 " pdb=" CD GLU B 57 " pdb=" OE1 GLU B 57 " ideal model delta sinusoidal sigma weight residual 0.00 89.36 -89.36 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CG ARG A 185 " pdb=" CD ARG A 185 " pdb=" NE ARG A 185 " pdb=" CZ ARG A 185 " ideal model delta sinusoidal sigma weight residual -180.00 -136.72 -43.28 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CB MET A 520 " pdb=" CG MET A 520 " pdb=" SD MET A 520 " pdb=" CE MET A 520 " ideal model delta sinusoidal sigma weight residual -60.00 -116.95 56.95 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 5167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 825 0.076 - 0.151: 63 0.151 - 0.227: 0 0.227 - 0.303: 1 0.303 - 0.379: 3 Chirality restraints: 892 Sorted by residual: chirality pdb=" C17 CLR A 801 " pdb=" C13 CLR A 801 " pdb=" C16 CLR A 801 " pdb=" C20 CLR A 801 " both_signs ideal model delta sigma weight residual False 2.55 2.93 -0.38 2.00e-01 2.50e+01 3.58e+00 chirality pdb=" C20 CLR A 801 " pdb=" C17 CLR A 801 " pdb=" C21 CLR A 801 " pdb=" C22 CLR A 801 " both_signs ideal model delta sigma weight residual False 2.59 2.94 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C13 CLR A 801 " pdb=" C12 CLR A 801 " pdb=" C14 CLR A 801 " pdb=" C17 CLR A 801 " both_signs ideal model delta sigma weight residual False -2.93 -3.25 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 889 not shown) Planarity restraints: 1566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 35 " -0.252 2.00e-02 2.50e+03 3.12e-01 1.46e+03 pdb=" CG ASN B 35 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 35 " 0.242 2.00e-02 2.50e+03 pdb=" ND2 ASN B 35 " 0.006 2.00e-02 2.50e+03 pdb="HD21 ASN B 35 " -0.489 2.00e-02 2.50e+03 pdb="HD22 ASN B 35 " 0.473 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 98 " 0.510 9.50e-02 1.11e+02 2.08e-01 3.51e+02 pdb=" NE ARG B 98 " 0.141 2.00e-02 2.50e+03 pdb=" CZ ARG B 98 " 0.041 2.00e-02 2.50e+03 pdb=" NH1 ARG B 98 " -0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG B 98 " -0.016 2.00e-02 2.50e+03 pdb="HH11 ARG B 98 " -0.199 2.00e-02 2.50e+03 pdb="HH12 ARG B 98 " 0.108 2.00e-02 2.50e+03 pdb="HH21 ARG B 98 " -0.200 2.00e-02 2.50e+03 pdb="HH22 ARG B 98 " 0.123 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 99 " -0.011 2.00e-02 2.50e+03 1.29e-02 2.50e+00 pdb=" CG ASN B 99 " -0.004 2.00e-02 2.50e+03 pdb=" OD1 ASN B 99 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN B 99 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN B 99 " -0.019 2.00e-02 2.50e+03 pdb="HD22 ASN B 99 " 0.018 2.00e-02 2.50e+03 ... (remaining 1563 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 118 2.08 - 2.71: 17621 2.71 - 3.34: 31989 3.34 - 3.97: 39383 3.97 - 4.60: 61842 Nonbonded interactions: 150953 Sorted by model distance: nonbonded pdb="HD22 ASN B 35 " pdb=" HE1 PHE B 109 " model vdw 1.450 2.100 nonbonded pdb="HE21 GLN A 547 " pdb=" O LEU A 558 " model vdw 1.632 2.450 nonbonded pdb=" OD1 ASN B 35 " pdb=" HB2 TRP B 50 " model vdw 1.669 2.620 nonbonded pdb="HE22 GLN A 552 " pdb=" OE1 GLU B 57 " model vdw 1.673 2.450 nonbonded pdb=" O PHE B 29 " pdb=" HG1 THR B 53 " model vdw 1.679 2.450 ... (remaining 150948 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 ========== 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 group one per residue 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: 4.130 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: 0.040 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 9.910 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 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 : 0.003 0.053 5453 Z= 0.163 Angle : 0.518 7.901 7438 Z= 0.276 Chirality : 0.044 0.379 892 Planarity : 0.005 0.121 909 Dihedral : 15.477 89.800 1952 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.52 % Allowed : 22.16 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.25 (0.34), residues: 684 helix: 3.58 (0.28), residues: 348 sheet: 1.34 (0.51), residues: 116 loop : 0.20 (0.42), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 98 TYR 0.005 0.001 TYR B 60 PHE 0.013 0.001 PHE A 508 TRP 0.003 0.000 TRP B 112 HIS 0.003 0.001 HIS A 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.16 ( 5450) covalent geometry : angle 0.51788 / 0.28 ( 7432) SS BOND : bond 0.00294 / 0.14 ( 3) SS BOND : angle 0.23774 / 0.13 ( 6) hydrogen bonds : bond 0.15111 / 9.16 ( 342) hydrogen bonds : angle 5.65358 / 4.08 ( 981) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 TRP cc_start: 0.8074 (m100) cc_final: 0.7320 (m100) REVERT: A 224 ARG cc_start: 0.6701 (mmp80) cc_final: 0.6266 (mtm180) REVERT: A 251 GLN cc_start: 0.7686 (mm-40) cc_final: 0.7482 (mt0) REVERT: A 356 LYS cc_start: 0.7410 (tppt) cc_final: 0.7039 (tppt) REVERT: A 385 LEU cc_start: 0.6036 (mt) cc_final: 0.5016 (tt) REVERT: A 527 MET cc_start: 0.7247 (mmp) cc_final: 0.6904 (mmp) REVERT: C 67 SER cc_start: 0.8175 (t) cc_final: 0.7968 (p) REVERT: C 71 SER cc_start: 0.7408 (t) cc_final: 0.7067 (m) outliers start: 3 outliers final: 1 residues processed: 139 average time/residue: 0.1297 time to fit residues: 23.6081 Evaluate side-chains 107 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 106 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 405 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.0980 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN C 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.191283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.165001 restraints weight = 16339.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.166799 restraints weight = 12727.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.172639 restraints weight = 10837.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.173625 restraints weight = 6881.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.176137 restraints weight = 5980.406| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5453 Z= 0.170 Angle : 0.537 5.841 7438 Z= 0.287 Chirality : 0.040 0.136 892 Planarity : 0.004 0.037 909 Dihedral : 4.006 41.251 794 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.55 % Allowed : 23.54 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.33), residues: 684 helix: 2.98 (0.27), residues: 357 sheet: 0.99 (0.50), residues: 116 loop : 0.15 (0.42), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 98 TYR 0.014 0.001 TYR C 53 PHE 0.016 0.001 PHE B 109 TRP 0.012 0.001 TRP B 50 HIS 0.005 0.002 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 ( 5450) covalent geometry : angle 0.53718 / 0.29 ( 7432) SS BOND : bond 0.00354 / 0.15 ( 3) SS BOND : angle 0.61087 / 0.29 ( 6) hydrogen bonds : bond 0.04381 / 2.88 ( 342) hydrogen bonds : angle 4.86523 / 3.55 ( 981) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 VAL cc_start: 0.8247 (t) cc_final: 0.7443 (t) REVERT: A 224 ARG cc_start: 0.6933 (mmp80) cc_final: 0.6374 (mtm180) REVERT: A 356 LYS cc_start: 0.7674 (tppt) cc_final: 0.7403 (tppt) REVERT: A 385 LEU cc_start: 0.6251 (mt) cc_final: 0.5153 (tt) REVERT: A 547 GLN cc_start: 0.6653 (mt0) cc_final: 0.6418 (mt0) outliers start: 9 outliers final: 8 residues processed: 112 average time/residue: 0.1005 time to fit residues: 15.7903 Evaluate side-chains 108 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 14 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 0.3980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 462 HIS ** 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 = 0.4106 r_free = 0.4106 target = 0.187402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.162547 restraints weight = 16326.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.166629 restraints weight = 11521.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.169911 restraints weight = 8438.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.170318 restraints weight = 6202.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.172678 restraints weight = 5910.083| |-----------------------------------------------------------------------------| r_work (final): 0.3958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5453 Z= 0.142 Angle : 0.497 5.918 7438 Z= 0.265 Chirality : 0.039 0.140 892 Planarity : 0.004 0.036 909 Dihedral : 4.506 59.516 793 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.41 % Allowed : 22.51 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.63 (0.33), residues: 684 helix: 3.02 (0.27), residues: 357 sheet: 1.15 (0.56), residues: 93 loop : -0.06 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 67 TYR 0.010 0.001 TYR C 53 PHE 0.014 0.001 PHE A 508 TRP 0.012 0.001 TRP B 50 HIS 0.005 0.002 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 ( 5450) covalent geometry : angle 0.49735 / 0.26 ( 7432) SS BOND : bond 0.00263 / 0.10 ( 3) SS BOND : angle 0.61132 / 0.30 ( 6) hydrogen bonds : bond 0.04446 / 2.90 ( 342) hydrogen bonds : angle 4.66155 / 3.42 ( 981) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 ASP cc_start: 0.7924 (t0) cc_final: 0.7647 (t0) REVERT: A 199 TRP cc_start: 0.8210 (m100) cc_final: 0.7826 (m100) REVERT: A 224 ARG cc_start: 0.6997 (mmp80) cc_final: 0.6339 (mtm180) REVERT: A 251 GLN cc_start: 0.7700 (mm-40) cc_final: 0.7446 (mt0) REVERT: A 356 LYS cc_start: 0.7710 (tppt) cc_final: 0.7269 (mptt) REVERT: A 547 GLN cc_start: 0.6977 (mt0) cc_final: 0.6639 (mt0) REVERT: A 558 LEU cc_start: 0.7854 (mt) cc_final: 0.7600 (mt) outliers start: 14 outliers final: 12 residues processed: 116 average time/residue: 0.1008 time to fit residues: 16.3254 Evaluate side-chains 115 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 96 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 42 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 462 HIS ** 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 = 0.3788 r_free = 0.3788 target = 0.165082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.134967 restraints weight = 17028.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.138958 restraints weight = 11463.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.139915 restraints weight = 8786.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.142643 restraints weight = 7484.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.142907 restraints weight = 6405.466| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5453 Z= 0.175 Angle : 0.534 5.988 7438 Z= 0.289 Chirality : 0.040 0.149 892 Planarity : 0.004 0.039 909 Dihedral : 4.518 40.014 793 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.26 % Allowed : 22.34 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.33), residues: 684 helix: 2.73 (0.27), residues: 363 sheet: 0.89 (0.57), residues: 93 loop : -0.22 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.011 0.002 TYR C 53 PHE 0.012 0.001 PHE B 109 TRP 0.016 0.001 TRP B 50 HIS 0.008 0.002 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.17 ( 5450) covalent geometry : angle 0.53379 / 0.29 ( 7432) SS BOND : bond 0.00270 / 0.10 ( 3) SS BOND : angle 1.02424 / 0.51 ( 6) hydrogen bonds : bond 0.04625 / 3.11 ( 342) hydrogen bonds : angle 4.68098 / 3.45 ( 981) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.7211 (mmp80) cc_final: 0.6525 (mtm180) REVERT: A 251 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7521 (mt0) REVERT: A 356 LYS cc_start: 0.7632 (tppt) cc_final: 0.7271 (mptt) REVERT: B 10 GLU cc_start: 0.7682 (mm-30) cc_final: 0.6910 (mm-30) outliers start: 19 outliers final: 17 residues processed: 122 average time/residue: 0.0987 time to fit residues: 17.0998 Evaluate side-chains 119 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 102 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 69 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 55 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 14 optimal weight: 0.0980 chunk 62 optimal weight: 0.1980 chunk 48 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.183840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.159624 restraints weight = 16402.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.164306 restraints weight = 10679.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.167296 restraints weight = 7878.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.169800 restraints weight = 6310.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.171113 restraints weight = 5249.541| |-----------------------------------------------------------------------------| r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5453 Z= 0.116 Angle : 0.477 5.933 7438 Z= 0.252 Chirality : 0.038 0.132 892 Planarity : 0.004 0.035 909 Dihedral : 4.286 38.765 793 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.75 % Allowed : 23.20 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.33), residues: 684 helix: 2.84 (0.28), residues: 364 sheet: 0.93 (0.56), residues: 93 loop : -0.18 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 576 TYR 0.009 0.001 TYR C 53 PHE 0.014 0.001 PHE A 508 TRP 0.009 0.001 TRP B 50 HIS 0.004 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 5450) covalent geometry : angle 0.47647 / 0.25 ( 7432) SS BOND : bond 0.00328 / 0.12 ( 3) SS BOND : angle 0.53689 / 0.24 ( 6) hydrogen bonds : bond 0.04184 / 2.77 ( 342) hydrogen bonds : angle 4.45859 / 3.29 ( 981) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.210 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 VAL cc_start: 0.8025 (OUTLIER) cc_final: 0.7773 (t) REVERT: A 224 ARG cc_start: 0.7202 (mmp80) cc_final: 0.6532 (mtm180) REVERT: A 251 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7481 (mt0) REVERT: A 356 LYS cc_start: 0.7700 (tppt) cc_final: 0.7494 (mptt) REVERT: A 530 LEU cc_start: 0.7791 (OUTLIER) cc_final: 0.7201 (tt) REVERT: A 547 GLN cc_start: 0.7224 (mt0) cc_final: 0.6788 (mt0) outliers start: 16 outliers final: 13 residues processed: 118 average time/residue: 0.0887 time to fit residues: 15.0560 Evaluate side-chains 114 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 99 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 405 SER Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 69 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 43 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 54 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 HIS ** 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 = 0.3983 r_free = 0.3983 target = 0.181368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.154312 restraints weight = 16800.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.155908 restraints weight = 12783.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.159009 restraints weight = 11577.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.159880 restraints weight = 8500.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.162681 restraints weight = 7788.654| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5453 Z= 0.157 Angle : 0.518 6.041 7438 Z= 0.277 Chirality : 0.039 0.138 892 Planarity : 0.004 0.036 909 Dihedral : 4.453 42.269 793 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.26 % Allowed : 22.34 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.21 (0.33), residues: 684 helix: 2.70 (0.28), residues: 364 sheet: 0.85 (0.57), residues: 93 loop : -0.36 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 98 TYR 0.010 0.001 TYR C 53 PHE 0.013 0.001 PHE A 508 TRP 0.011 0.001 TRP B 50 HIS 0.007 0.002 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 5450) covalent geometry : angle 0.51802 / 0.28 ( 7432) SS BOND : bond 0.00374 / 0.14 ( 3) SS BOND : angle 0.58097 / 0.26 ( 6) hydrogen bonds : bond 0.04450 / 2.99 ( 342) hydrogen bonds : angle 4.51869 / 3.34 ( 981) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 100 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7818 (t) REVERT: A 224 ARG cc_start: 0.7231 (mmp80) cc_final: 0.6525 (mtm180) REVERT: A 356 LYS cc_start: 0.7623 (tppt) cc_final: 0.7397 (mptt) REVERT: A 530 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.6974 (tt) REVERT: A 552 GLN cc_start: 0.7199 (mt0) cc_final: 0.6977 (mt0) outliers start: 19 outliers final: 16 residues processed: 116 average time/residue: 0.1009 time to fit residues: 16.9241 Evaluate side-chains 113 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 69 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 21 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 2 optimal weight: 0.0870 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.177697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.155049 restraints weight = 16231.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.158786 restraints weight = 10992.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.161706 restraints weight = 8226.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.163511 restraints weight = 6639.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.164998 restraints weight = 5645.119| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5453 Z= 0.152 Angle : 0.505 6.053 7438 Z= 0.271 Chirality : 0.039 0.142 892 Planarity : 0.004 0.042 909 Dihedral : 4.576 46.460 793 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.36 % Favored : 96.49 % Rotamer: Outliers : 3.95 % Allowed : 22.16 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.34), residues: 684 helix: 2.68 (0.28), residues: 363 sheet: 0.57 (0.55), residues: 104 loop : -0.31 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 424 TYR 0.010 0.001 TYR A 214 PHE 0.011 0.001 PHE A 508 TRP 0.033 0.001 TRP A 567 HIS 0.006 0.002 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 5450) covalent geometry : angle 0.50487 / 0.27 ( 7432) SS BOND : bond 0.00422 / 0.16 ( 3) SS BOND : angle 0.68928 / 0.31 ( 6) hydrogen bonds : bond 0.04380 / 2.94 ( 342) hydrogen bonds : angle 4.50285 / 3.32 ( 981) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 VAL cc_start: 0.8036 (OUTLIER) cc_final: 0.7811 (t) REVERT: A 224 ARG cc_start: 0.7217 (mmp80) cc_final: 0.6560 (mtm180) REVERT: A 530 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7020 (tt) REVERT: C 31 ASN cc_start: 0.7391 (OUTLIER) cc_final: 0.6825 (t0) outliers start: 23 outliers final: 18 residues processed: 116 average time/residue: 0.1046 time to fit residues: 17.2402 Evaluate side-chains 116 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 95 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 69 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 28 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 48 optimal weight: 0.1980 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.176428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.153410 restraints weight = 16483.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.157246 restraints weight = 11147.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.159923 restraints weight = 8421.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.162171 restraints weight = 6809.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.163402 restraints weight = 5756.500| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5453 Z= 0.156 Angle : 0.509 6.071 7438 Z= 0.276 Chirality : 0.039 0.138 892 Planarity : 0.004 0.035 909 Dihedral : 4.636 49.186 793 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.24 % Favored : 95.61 % Rotamer: Outliers : 3.61 % Allowed : 23.37 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.34), residues: 684 helix: 2.64 (0.28), residues: 363 sheet: 0.52 (0.54), residues: 104 loop : -0.42 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 424 TYR 0.009 0.001 TYR C 53 PHE 0.015 0.001 PHE B 95 TRP 0.014 0.001 TRP A 567 HIS 0.006 0.002 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 5450) covalent geometry : angle 0.50891 / 0.28 ( 7432) SS BOND : bond 0.00380 / 0.14 ( 3) SS BOND : angle 0.63212 / 0.29 ( 6) hydrogen bonds : bond 0.04452 / 2.99 ( 342) hydrogen bonds : angle 4.51562 / 3.33 ( 981) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.7240 (mmp80) cc_final: 0.6560 (mtm180) REVERT: A 530 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.6965 (tt) REVERT: B 91 THR cc_start: 0.8457 (t) cc_final: 0.8159 (p) outliers start: 21 outliers final: 19 residues processed: 114 average time/residue: 0.1142 time to fit residues: 18.2545 Evaluate side-chains 116 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain A residue 530 LEU Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 69 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 66 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 30 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN B 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.176493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.153464 restraints weight = 16353.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.157366 restraints weight = 11012.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.159904 restraints weight = 8269.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.162289 restraints weight = 6731.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.163553 restraints weight = 5663.467| |-----------------------------------------------------------------------------| r_work (final): 0.3890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5453 Z= 0.137 Angle : 0.498 6.075 7438 Z= 0.267 Chirality : 0.039 0.138 892 Planarity : 0.004 0.035 909 Dihedral : 4.588 50.102 793 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.95 % Favored : 95.91 % Rotamer: Outliers : 3.95 % Allowed : 23.71 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.34), residues: 684 helix: 2.66 (0.28), residues: 363 sheet: 0.53 (0.54), residues: 104 loop : -0.44 (0.41), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 424 TYR 0.009 0.001 TYR C 53 PHE 0.009 0.001 PHE B 95 TRP 0.022 0.001 TRP A 567 HIS 0.005 0.002 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 5450) covalent geometry : angle 0.49766 / 0.27 ( 7432) SS BOND : bond 0.00375 / 0.14 ( 3) SS BOND : angle 0.55486 / 0.26 ( 6) hydrogen bonds : bond 0.04319 / 2.90 ( 342) hydrogen bonds : angle 4.45846 / 3.29 ( 981) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 98 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.7271 (mmp80) cc_final: 0.6582 (mtm180) REVERT: C 31 ASN cc_start: 0.7434 (OUTLIER) cc_final: 0.6888 (t0) outliers start: 23 outliers final: 19 residues processed: 114 average time/residue: 0.1129 time to fit residues: 18.2000 Evaluate side-chains 116 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 96 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 69 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 6 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 5 optimal weight: 0.3980 chunk 42 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN B 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.176558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.153858 restraints weight = 16352.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.157508 restraints weight = 11028.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.160524 restraints weight = 8318.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.162218 restraints weight = 6707.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.163691 restraints weight = 5730.912| |-----------------------------------------------------------------------------| r_work (final): 0.3884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5453 Z= 0.138 Angle : 0.499 6.115 7438 Z= 0.269 Chirality : 0.039 0.138 892 Planarity : 0.004 0.035 909 Dihedral : 4.641 52.267 793 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.80 % Favored : 96.05 % Rotamer: Outliers : 3.78 % Allowed : 24.57 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.33), residues: 684 helix: 2.67 (0.28), residues: 364 sheet: 0.47 (0.54), residues: 104 loop : -0.45 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 424 TYR 0.009 0.001 TYR C 53 PHE 0.010 0.001 PHE B 95 TRP 0.021 0.001 TRP A 567 HIS 0.005 0.002 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 5450) covalent geometry : angle 0.49893 / 0.27 ( 7432) SS BOND : bond 0.00384 / 0.15 ( 3) SS BOND : angle 0.55474 / 0.27 ( 6) hydrogen bonds : bond 0.04316 / 2.90 ( 342) hydrogen bonds : angle 4.44100 / 3.28 ( 981) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1368 Ramachandran restraints generated. 684 Oldfield, 0 Emsley, 684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 95 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 224 ARG cc_start: 0.7292 (mmp80) cc_final: 0.6588 (mtm180) REVERT: C 31 ASN cc_start: 0.7497 (OUTLIER) cc_final: 0.6951 (t0) outliers start: 22 outliers final: 19 residues processed: 111 average time/residue: 0.1093 time to fit residues: 17.1947 Evaluate side-chains 114 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 409 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 441 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 100 TYR Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 31 ASN Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 69 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 47 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.2980 chunk 13 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 495 GLN B 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.161874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.128603 restraints weight = 17252.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.134084 restraints weight = 10822.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.138120 restraints weight = 7848.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.140673 restraints weight = 6250.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.142710 restraints weight = 5296.982| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5453 Z= 0.145 Angle : 0.510 6.108 7438 Z= 0.274 Chirality : 0.039 0.137 892 Planarity : 0.004 0.034 909 Dihedral : 4.708 54.428 793 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.95 % Favored : 95.91 % Rotamer: Outliers : 4.12 % Allowed : 24.57 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.34), residues: 684 helix: 2.63 (0.28), residues: 364 sheet: 0.48 (0.54), residues: 104 loop : -0.48 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 424 TYR 0.009 0.001 TYR C 53 PHE 0.010 0.001 PHE B 95 TRP 0.023 0.001 TRP A 567 HIS 0.006 0.002 HIS C 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 ( 5450) covalent geometry : angle 0.51024 / 0.27 ( 7432) SS BOND : bond 0.00418 / 0.16 ( 3) SS BOND : angle 0.65739 / 0.31 ( 6) hydrogen bonds : bond 0.04357 / 2.93 ( 342) hydrogen bonds : angle 4.46676 / 3.30 ( 981) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1802.90 seconds wall clock time: 31 minutes 16.98 seconds (1876.98 seconds total)