Starting phenix.real_space_refine on Fri Feb 14 09:03:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fgx_29077/02_2025/8fgx_29077_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fgx_29077/02_2025/8fgx_29077.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fgx_29077/02_2025/8fgx_29077.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fgx_29077/02_2025/8fgx_29077.map" model { file = "/net/cci-nas-00/data/ceres_data/8fgx_29077/02_2025/8fgx_29077_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fgx_29077/02_2025/8fgx_29077_trim.cif" } resolution = 2.62 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= -0.000 sd= 0.000 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 22 5.16 5 C 3186 2.51 5 N 838 2.21 5 O 980 1.98 5 H 4873 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9899 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 3252 Classifications: {'peptide': 213} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "B" Number of atoms: 3190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3190 Classifications: {'peptide': 216} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 202} Chain breaks: 1 Chain: "C" Number of atoms: 3415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 3415 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain breaks: 3 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.69, per 1000 atoms: 0.57 Number of scatterers: 9899 At special positions: 0 Unit cell: (106.683, 99.24, 83.527, 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 22 16.00 O 980 8.00 N 838 7.00 C 3186 6.00 H 4873 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 148 " - pdb=" SG CYS B 204 " distance=2.03 Simple disulfide: pdb=" SG CYS C 419 " - pdb=" SG CYS C 435 " distance=2.03 Simple disulfide: pdb=" SG CYS C 517 " - pdb=" SG CYS C 584 " distance=2.03 Simple disulfide: pdb=" SG CYS C 548 " - pdb=" SG CYS C 563 " 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 Links applied NAG-ASN " NAG C 701 " - " ASN C 396 " " NAG C 702 " - " ASN C 453 " " NAG C 703 " - " ASN C 494 " Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 676.8 milliseconds 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1184 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 13 sheets defined 11.3% alpha, 46.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 3.701A pdb=" N PHE A 83 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.686A pdb=" N SER A 127 " --> pdb=" O GLU A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.727A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 195 through 199 Processing helix chain 'B' and resid 209 through 212 Processing helix chain 'C' and resid 432 through 437 Processing helix chain 'C' and resid 453 through 457 Processing helix chain 'C' and resid 506 through 511 removed outlier: 3.812A pdb=" N THR C 510 " --> pdb=" O LYS C 507 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER C 511 " --> pdb=" O GLY C 508 " (cutoff:3.500A) Processing helix chain 'C' and resid 544 through 550 removed outlier: 4.006A pdb=" N LYS C 550 " --> pdb=" O GLU C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 626 Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.419A pdb=" N LEU A 11 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 33 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR A 49 " --> pdb=" O VAL A 33 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.419A pdb=" N LEU A 11 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR A 97 " --> pdb=" O GLN A 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 118 removed outlier: 4.963A pdb=" N SER A 131 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU A 181 " --> pdb=" O SER A 131 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N VAL A 133 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N LEU A 179 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N LEU A 135 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER A 177 " --> pdb=" O LEU A 135 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASN A 137 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU A 175 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AA6, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.415A pdb=" N MET B 34 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.684A pdb=" N CYS B 96 " --> pdb=" O TRP B 111 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N TRP B 111 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N GLY B 98 " --> pdb=" O ASP B 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.061A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.061A pdb=" N TYR B 184 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 162 removed outlier: 4.313A pdb=" N TYR B 202 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 405 through 410 removed outlier: 6.903A pdb=" N VAL C 410 " --> pdb=" O HIS C 417 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N HIS C 417 " --> pdb=" O VAL C 410 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU C 486 " --> pdb=" O ILE C 469 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE C 469 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N LYS C 488 " --> pdb=" O LYS C 467 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE C 466 " --> pdb=" O TRP C 445 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TRP C 445 " --> pdb=" O ILE C 466 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 536 through 539 removed outlier: 3.727A pdb=" N THR C 520 " --> pdb=" O PRO C 581 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU C 582 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N CYS C 563 " --> pdb=" O VAL C 543 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 486 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: 3.78 Time building geometry restraints manager: 3.19 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: 4858 1.03 - 1.23: 18 1.23 - 1.42: 2174 1.42 - 1.61: 2942 1.61 - 1.81: 29 Bond restraints: 10021 Sorted by residual: bond pdb=" N ILE C 391 " pdb=" CA ILE C 391 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.58e+00 bond pdb=" N ILE C 391 " pdb=" H ILE C 391 " ideal model delta sigma weight residual 0.860 0.888 -0.028 2.00e-02 2.50e+03 1.98e+00 bond pdb=" C1 NAG C 702 " pdb=" O5 NAG C 702 " ideal model delta sigma weight residual 1.406 1.431 -0.025 2.00e-02 2.50e+03 1.59e+00 bond pdb=" C1 NAG C 701 " pdb=" O5 NAG C 701 " ideal model delta sigma weight residual 1.406 1.430 -0.024 2.00e-02 2.50e+03 1.46e+00 bond pdb=" C1 NAG C 703 " pdb=" O5 NAG C 703 " ideal model delta sigma weight residual 1.406 1.429 -0.023 2.00e-02 2.50e+03 1.37e+00 ... (remaining 10016 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 16789 0.92 - 1.84: 1181 1.84 - 2.76: 45 2.76 - 3.68: 25 3.68 - 4.60: 3 Bond angle restraints: 18043 Sorted by residual: angle pdb=" CA PRO C 608 " pdb=" C PRO C 608 " pdb=" N GLY C 609 " ideal model delta sigma weight residual 114.66 116.82 -2.16 1.34e+00 5.57e-01 2.60e+00 angle pdb=" CA ILE C 391 " pdb=" N ILE C 391 " pdb=" H ILE C 391 " ideal model delta sigma weight residual 114.00 109.40 4.60 3.00e+00 1.11e-01 2.35e+00 angle pdb=" N ALA A 51 " pdb=" CA ALA A 51 " pdb=" C ALA A 51 " ideal model delta sigma weight residual 110.80 114.05 -3.25 2.13e+00 2.20e-01 2.33e+00 angle pdb=" N SER C 597 " pdb=" CA SER C 597 " pdb=" C SER C 597 " ideal model delta sigma weight residual 113.18 111.31 1.87 1.33e+00 5.65e-01 1.98e+00 angle pdb=" C TYR A 50 " pdb=" N ALA A 51 " pdb=" CA ALA A 51 " ideal model delta sigma weight residual 121.54 124.17 -2.63 1.91e+00 2.74e-01 1.90e+00 ... (remaining 18038 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 4525 17.41 - 34.81: 173 34.81 - 52.22: 88 52.22 - 69.62: 40 69.62 - 87.03: 15 Dihedral angle restraints: 4841 sinusoidal: 2631 harmonic: 2210 Sorted by residual: dihedral pdb=" CA ARG A 142 " pdb=" C ARG A 142 " pdb=" N GLU A 143 " pdb=" CA GLU A 143 " ideal model delta harmonic sigma weight residual -180.00 -162.97 -17.03 0 5.00e+00 4.00e-02 1.16e+01 dihedral pdb=" CA PHE B 95 " pdb=" C PHE B 95 " pdb=" N CYS B 96 " pdb=" CA CYS B 96 " ideal model delta harmonic sigma weight residual 180.00 163.71 16.29 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 68.07 24.93 1 1.00e+01 1.00e-02 8.94e+00 ... (remaining 4838 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 504 0.033 - 0.065: 187 0.065 - 0.097: 37 0.097 - 0.130: 58 0.130 - 0.162: 2 Chirality restraints: 788 Sorted by residual: chirality pdb=" C1 NAG C 703 " pdb=" ND2 ASN C 494 " pdb=" C2 NAG C 703 " pdb=" O5 NAG C 703 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA ILE C 531 " pdb=" N ILE C 531 " pdb=" C ILE C 531 " pdb=" CB ILE C 531 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA ILE A 21 " pdb=" N ILE A 21 " pdb=" C ILE A 21 " pdb=" CB ILE A 21 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 785 not shown) Planarity restraints: 1491 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 607 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO C 608 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 608 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 608 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 156 " -0.022 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO B 157 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 157 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 157 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 209 " -0.017 5.00e-02 4.00e+02 2.52e-02 1.02e+00 pdb=" N PRO B 210 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO B 210 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO B 210 " -0.014 5.00e-02 4.00e+02 ... (remaining 1488 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 849 2.22 - 2.82: 21627 2.82 - 3.41: 25899 3.41 - 4.01: 38020 4.01 - 4.60: 56223 Nonbonded interactions: 142618 Sorted by model distance: nonbonded pdb=" OE1 GLU A 123 " pdb=" H GLU A 123 " model vdw 1.630 2.450 nonbonded pdb=" HH TYR A 36 " pdb=" OE1 GLN A 89 " model vdw 1.633 2.450 nonbonded pdb=" O ASP A 82 " pdb=" HH TYR A 86 " model vdw 1.648 2.450 nonbonded pdb="HE22 GLN B 6 " pdb=" O TYR B 94 " model vdw 1.665 2.450 nonbonded pdb=" OE1 GLN C 409 " pdb="HE21 GLN C 415 " model vdw 1.671 2.450 ... (remaining 142613 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 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: 0.150 Extract box with map and model: 0.450 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 25.660 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 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 0.031 5148 Z= 0.184 Angle : 0.446 4.136 7002 Z= 0.230 Chirality : 0.044 0.162 788 Planarity : 0.003 0.041 883 Dihedral : 9.989 87.028 1879 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.41 (0.36), residues: 631 helix: -0.33 (0.92), residues: 33 sheet: 0.66 (0.31), residues: 270 loop : 1.58 (0.40), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 111 HIS 0.002 0.001 HIS A 198 PHE 0.010 0.001 PHE A 46 TYR 0.006 0.001 TYR A 91 ARG 0.002 0.000 ARG B 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 3.4948 time to fit residues: 209.4767 Evaluate side-chains 42 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 0.0370 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 overall best weight: 0.8462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 HIS B 50 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.052178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.039046 restraints weight = 47707.852| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 3.26 r_work: 0.2549 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2425 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5148 Z= 0.229 Angle : 0.509 4.432 7002 Z= 0.274 Chirality : 0.045 0.154 788 Planarity : 0.004 0.036 883 Dihedral : 5.245 41.739 745 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.18 % Allowed : 6.29 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.35), residues: 631 helix: -0.27 (0.81), residues: 33 sheet: 0.61 (0.30), residues: 277 loop : 1.43 (0.39), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 428 HIS 0.004 0.001 HIS C 434 PHE 0.013 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.005 0.001 ARG B 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 43 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.9221 (tt0) cc_final: 0.8894 (tt0) outliers start: 1 outliers final: 0 residues processed: 43 average time/residue: 3.1514 time to fit residues: 140.8148 Evaluate side-chains 39 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 58 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.3088 r_free = 0.3088 target = 0.051131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.038058 restraints weight = 48443.064| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 3.23 r_work: 0.2536 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5148 Z= 0.232 Angle : 0.494 4.653 7002 Z= 0.263 Chirality : 0.045 0.146 788 Planarity : 0.004 0.034 883 Dihedral : 4.810 35.114 745 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.18 % Allowed : 6.83 % Favored : 92.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.20 (0.34), residues: 631 helix: -0.16 (0.82), residues: 34 sheet: 0.62 (0.29), residues: 274 loop : 1.31 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 428 HIS 0.002 0.001 HIS C 434 PHE 0.010 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.003 0.001 ARG C 416 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7972 (mm-30) REVERT: A 195 GLU cc_start: 0.9199 (tt0) cc_final: 0.8930 (tt0) REVERT: C 497 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8714 (mp0) outliers start: 1 outliers final: 0 residues processed: 40 average time/residue: 2.8386 time to fit residues: 118.4911 Evaluate side-chains 38 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 20 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3083 r_free = 0.3083 target = 0.050831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.037807 restraints weight = 48009.496| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 3.22 r_work: 0.2529 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2407 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5148 Z= 0.227 Angle : 0.490 4.488 7002 Z= 0.260 Chirality : 0.045 0.148 788 Planarity : 0.003 0.035 883 Dihedral : 4.551 30.182 745 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.34), residues: 631 helix: -0.04 (0.87), residues: 34 sheet: 0.66 (0.30), residues: 274 loop : 1.27 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 PHE 0.011 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.002 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8019 (mm-30) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 2.8038 time to fit residues: 122.8889 Evaluate side-chains 40 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 18 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3082 r_free = 0.3082 target = 0.050750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.037806 restraints weight = 48677.090| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 3.21 r_work: 0.2534 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5148 Z= 0.228 Angle : 0.492 4.652 7002 Z= 0.260 Chirality : 0.044 0.149 788 Planarity : 0.003 0.037 883 Dihedral : 4.363 26.867 745 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.20 (0.34), residues: 631 helix: -0.03 (0.87), residues: 34 sheet: 0.69 (0.30), residues: 274 loop : 1.22 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 PHE 0.011 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.003 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.9186 (tt0) cc_final: 0.8846 (tt0) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 2.7846 time to fit residues: 119.3131 Evaluate side-chains 38 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 27 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.1782 ------------------------------------------------------------------------------- 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 = 0.3069 r_free = 0.3069 target = 0.050208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.037271 restraints weight = 48951.746| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 3.21 r_work: 0.2513 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2392 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5148 Z= 0.291 Angle : 0.514 5.257 7002 Z= 0.271 Chirality : 0.045 0.150 788 Planarity : 0.003 0.039 883 Dihedral : 4.306 24.336 745 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.36 % Allowed : 7.73 % Favored : 91.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.34), residues: 631 helix: -0.06 (0.84), residues: 34 sheet: 0.67 (0.30), residues: 272 loop : 1.16 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 PHE 0.012 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.002 0.000 ARG A 211 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7985 (mm-30) REVERT: A 195 GLU cc_start: 0.9195 (tt0) cc_final: 0.8895 (tt0) REVERT: C 551 ARG cc_start: 0.9096 (mtp85) cc_final: 0.8852 (tpt170) REVERT: C 554 ASP cc_start: 0.9001 (m-30) cc_final: 0.8225 (p0) REVERT: C 555 TYR cc_start: 0.7539 (m-80) cc_final: 0.6096 (m-80) REVERT: C 623 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8418 (pp20) outliers start: 2 outliers final: 0 residues processed: 44 average time/residue: 2.9663 time to fit residues: 135.8903 Evaluate side-chains 38 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 48 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 9 optimal weight: 0.0980 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3084 r_free = 0.3084 target = 0.050689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.037762 restraints weight = 49218.290| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 3.23 r_work: 0.2536 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2416 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5148 Z= 0.196 Angle : 0.504 5.614 7002 Z= 0.265 Chirality : 0.044 0.152 788 Planarity : 0.003 0.038 883 Dihedral : 4.173 23.275 745 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.34), residues: 631 helix: 0.09 (0.88), residues: 35 sheet: 0.75 (0.30), residues: 271 loop : 1.15 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 PHE 0.010 0.001 PHE B 95 TYR 0.007 0.001 TYR A 49 ARG 0.005 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.9184 (tt0) cc_final: 0.8898 (tt0) REVERT: C 554 ASP cc_start: 0.8989 (m-30) cc_final: 0.8244 (p0) REVERT: C 555 TYR cc_start: 0.7577 (m-80) cc_final: 0.6176 (m-80) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 2.7944 time to fit residues: 117.0211 Evaluate side-chains 38 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 43 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 48 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 = 0.3081 r_free = 0.3081 target = 0.050472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2667 r_free = 0.2667 target = 0.037542 restraints weight = 48776.476| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 3.23 r_work: 0.2533 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2413 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5148 Z= 0.198 Angle : 0.522 6.710 7002 Z= 0.274 Chirality : 0.045 0.151 788 Planarity : 0.003 0.039 883 Dihedral : 4.077 23.147 745 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.34), residues: 631 helix: -0.13 (0.88), residues: 35 sheet: 0.78 (0.30), residues: 271 loop : 1.17 (0.37), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 PHE 0.009 0.001 PHE B 95 TYR 0.006 0.001 TYR A 49 ARG 0.005 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.9173 (tt0) cc_final: 0.8889 (tt0) REVERT: C 554 ASP cc_start: 0.8961 (m-30) cc_final: 0.8405 (p0) REVERT: C 555 TYR cc_start: 0.7631 (m-80) cc_final: 0.6206 (m-80) REVERT: C 623 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8376 (pp20) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 2.7074 time to fit residues: 119.0268 Evaluate side-chains 38 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 0.0670 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.3092 r_free = 0.3092 target = 0.050884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.037797 restraints weight = 49390.664| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 3.29 r_work: 0.2538 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2418 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5148 Z= 0.203 Angle : 0.512 6.285 7002 Z= 0.269 Chirality : 0.044 0.152 788 Planarity : 0.003 0.039 883 Dihedral : 4.039 23.075 745 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.34), residues: 631 helix: -0.37 (0.84), residues: 39 sheet: 0.80 (0.30), residues: 271 loop : 1.20 (0.37), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 PHE 0.009 0.001 PHE B 95 TYR 0.006 0.001 TYR A 49 ARG 0.006 0.000 ARG A 142 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.9175 (tt0) cc_final: 0.8896 (tt0) REVERT: C 554 ASP cc_start: 0.9160 (m-30) cc_final: 0.8448 (p0) REVERT: C 623 GLU cc_start: 0.8666 (tm-30) cc_final: 0.8370 (pp20) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 2.6512 time to fit residues: 99.9652 Evaluate side-chains 36 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 16 optimal weight: 0.2980 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.3098 r_free = 0.3098 target = 0.051133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.038018 restraints weight = 49098.007| |-----------------------------------------------------------------------------| r_work (start): 0.2663 rms_B_bonded: 3.29 r_work: 0.2547 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2427 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5148 Z= 0.184 Angle : 0.507 6.538 7002 Z= 0.266 Chirality : 0.044 0.153 788 Planarity : 0.003 0.039 883 Dihedral : 3.953 23.445 745 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 10.43 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % 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: 1.30 (0.34), residues: 631 helix: -0.22 (0.88), residues: 39 sheet: 0.85 (0.30), residues: 271 loop : 1.23 (0.38), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 PHE 0.008 0.001 PHE B 95 TYR 0.006 0.001 TYR A 49 ARG 0.006 0.000 ARG A 142 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1262 Ramachandran restraints generated. 631 Oldfield, 0 Emsley, 631 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 GLU cc_start: 0.9170 (tt0) cc_final: 0.8892 (tt0) REVERT: C 554 ASP cc_start: 0.9116 (m-30) cc_final: 0.8429 (p0) REVERT: C 555 TYR cc_start: 0.7683 (m-80) cc_final: 0.6278 (m-80) REVERT: C 623 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8371 (pp20) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 2.6352 time to fit residues: 102.3352 Evaluate side-chains 37 residues out of total 556 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 40 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3088 r_free = 0.3088 target = 0.050755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.037586 restraints weight = 49196.933| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 3.30 r_work: 0.2534 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2414 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 5148 Z= 0.215 Angle : 0.509 6.459 7002 Z= 0.267 Chirality : 0.044 0.153 788 Planarity : 0.003 0.039 883 Dihedral : 3.963 23.358 745 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.34), residues: 631 helix: -0.19 (0.86), residues: 39 sheet: 0.81 (0.30), residues: 271 loop : 1.21 (0.38), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 47 HIS 0.002 0.001 HIS A 53 PHE 0.010 0.001 PHE B 95 TYR 0.006 0.001 TYR A 49 ARG 0.006 0.000 ARG A 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8234.41 seconds wall clock time: 145 minutes 21.83 seconds (8721.83 seconds total)