Starting phenix.real_space_refine on Thu Mar 6 03:54:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7swo_25477/03_2025/7swo_25477_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swo_25477/03_2025/7swo_25477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7swo_25477/03_2025/7swo_25477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swo_25477/03_2025/7swo_25477.map" model { file = "/net/cci-nas-00/data/ceres_data/7swo_25477/03_2025/7swo_25477_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swo_25477/03_2025/7swo_25477_neut.cif" } resolution = 4.1 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= 0.002 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 3020 2.51 5 N 804 2.21 5 O 940 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4784 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1545 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "H" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1616 Classifications: {'peptide': 219} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 207} Chain: "L" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1623 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Time building chain proxies: 3.50, per 1000 atoms: 0.73 Number of scatterers: 4784 At special positions: 0 Unit cell: (81.675, 72.6, 122.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 940 8.00 N 804 7.00 C 3020 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.04 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: 1.13 Conformation dependent library (CDL) restraints added in 570.5 milliseconds 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1148 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 11 sheets defined 12.4% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.825A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 411 Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.514A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.523A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.800A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.607A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 135 removed outlier: 3.655A pdb=" N THR H 135 " --> pdb=" O SER H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 189 through 194 removed outlier: 4.149A pdb=" N GLY H 194 " --> pdb=" O SER H 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'L' and resid 121 through 126 Processing helix chain 'L' and resid 183 through 189 removed outlier: 3.902A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 379 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.663A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.890A pdb=" N TYR H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ALA H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLY H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 125 through 128 removed outlier: 5.638A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 155 through 158 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 removed outlier: 6.587A pdb=" N THR L 70 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.917A pdb=" N GLN L 27 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 10.188A pdb=" N SER L 68 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.355A pdb=" N VAL L 29 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 11.926A pdb=" N SER L 66 " --> pdb=" O VAL L 29 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.557A pdb=" N TYR L 87 " --> pdb=" O THR L 102 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 116 through 118 removed outlier: 5.228A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 144 through 150 153 hydrogen bonds defined for protein. 363 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: 1.39 Time building geometry restraints manager: 1.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 1518 1.34 - 1.46: 1112 1.46 - 1.58: 2246 1.58 - 1.70: 0 1.70 - 1.82: 23 Bond restraints: 4899 Sorted by residual: bond pdb=" N ILE L 106 " pdb=" CA ILE L 106 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.10e-02 8.26e+03 9.54e+00 bond pdb=" N LYS H 147 " pdb=" CA LYS H 147 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.21e-02 6.83e+03 6.53e+00 bond pdb=" N ARG L 108 " pdb=" CA ARG L 108 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.20e-02 6.94e+03 5.90e+00 bond pdb=" N GLU L 123 " pdb=" CA GLU L 123 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.40e+00 bond pdb=" N TYR L 87 " pdb=" CA TYR L 87 " ideal model delta sigma weight residual 1.456 1.485 -0.028 1.23e-02 6.61e+03 5.35e+00 ... (remaining 4894 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 6369 1.93 - 3.86: 243 3.86 - 5.79: 44 5.79 - 7.72: 8 7.72 - 9.65: 1 Bond angle restraints: 6665 Sorted by residual: angle pdb=" N THR L 109 " pdb=" CA THR L 109 " pdb=" C THR L 109 " ideal model delta sigma weight residual 110.35 105.09 5.26 1.40e+00 5.10e-01 1.41e+01 angle pdb=" C ASP A 420 " pdb=" N TYR A 421 " pdb=" CA TYR A 421 " ideal model delta sigma weight residual 122.58 114.99 7.59 2.07e+00 2.33e-01 1.34e+01 angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 107.88 112.96 -5.08 1.41e+00 5.03e-01 1.30e+01 angle pdb=" N GLU L 123 " pdb=" CA GLU L 123 " pdb=" C GLU L 123 " ideal model delta sigma weight residual 111.33 107.12 4.21 1.21e+00 6.83e-01 1.21e+01 angle pdb=" N LYS L 107 " pdb=" CA LYS L 107 " pdb=" C LYS L 107 " ideal model delta sigma weight residual 110.24 105.84 4.40 1.47e+00 4.63e-01 8.95e+00 ... (remaining 6660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 2604 17.69 - 35.38: 252 35.38 - 53.07: 48 53.07 - 70.75: 7 70.75 - 88.44: 6 Dihedral angle restraints: 2917 sinusoidal: 1111 harmonic: 1806 Sorted by residual: dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 40.97 52.03 1 1.00e+01 1.00e-02 3.69e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -45.72 -40.28 1 1.00e+01 1.00e-02 2.28e+01 dihedral pdb=" CA TYR A 365 " pdb=" C TYR A 365 " pdb=" N SER A 366 " pdb=" CA SER A 366 " ideal model delta harmonic sigma weight residual -180.00 -157.92 -22.08 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 2914 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 497 0.046 - 0.091: 176 0.091 - 0.136: 52 0.136 - 0.182: 12 0.182 - 0.227: 4 Chirality restraints: 741 Sorted by residual: chirality pdb=" CB VAL H 100 " pdb=" CA VAL H 100 " pdb=" CG1 VAL H 100 " pdb=" CG2 VAL H 100 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE H 27 " pdb=" CA ILE H 27 " pdb=" CG1 ILE H 27 " pdb=" CG2 ILE H 27 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA VAL H 154 " pdb=" N VAL H 154 " pdb=" C VAL H 154 " pdb=" CB VAL H 154 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.90e-01 ... (remaining 738 not shown) Planarity restraints: 860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 126 " -0.062 5.00e-02 4.00e+02 9.43e-02 1.42e+01 pdb=" N PRO H 127 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO H 127 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO H 127 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL L 86 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C VAL L 86 " 0.042 2.00e-02 2.50e+03 pdb=" O VAL L 86 " -0.016 2.00e-02 2.50e+03 pdb=" N TYR L 87 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 453 " 0.023 2.00e-02 2.50e+03 1.65e-02 5.43e+00 pdb=" CG TYR A 453 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR A 453 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR A 453 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 453 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 453 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 453 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 453 " 0.003 2.00e-02 2.50e+03 ... (remaining 857 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 803 2.75 - 3.29: 4862 3.29 - 3.83: 7985 3.83 - 4.36: 9445 4.36 - 4.90: 15953 Nonbonded interactions: 39048 Sorted by model distance: nonbonded pdb=" OG SER L 7 " pdb=" OG SER L 22 " model vdw 2.215 3.040 nonbonded pdb=" OG SER H 7 " pdb=" OG SER H 21 " model vdw 2.216 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.218 3.040 nonbonded pdb=" O GLN H 3 " pdb=" OG SER H 25 " model vdw 2.227 3.040 nonbonded pdb=" OG SER L 66 " pdb=" OG1 THR L 73 " model vdw 2.227 3.040 ... (remaining 39043 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.250 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 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 : 0.007 0.049 4899 Z= 0.440 Angle : 0.893 9.655 6665 Z= 0.486 Chirality : 0.053 0.227 741 Planarity : 0.006 0.094 860 Dihedral : 14.431 88.441 1745 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 26.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.98 % Favored : 90.02 % Rotamer: Outliers : 0.19 % Allowed : 0.93 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.34), residues: 621 helix: -2.41 (0.88), residues: 25 sheet: -1.33 (0.34), residues: 229 loop : -1.97 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 353 HIS 0.003 0.002 HIS A 519 PHE 0.022 0.002 PHE L 139 TYR 0.040 0.002 TYR A 453 ARG 0.005 0.001 ARG H 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 125 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8149 (mmt90) cc_final: 0.7920 (mmt90) REVERT: A 444 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7378 (mmtm) REVERT: A 458 LYS cc_start: 0.8902 (ttmt) cc_final: 0.8417 (tmtt) REVERT: A 465 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7563 (mt-10) REVERT: H 20 LEU cc_start: 0.6872 (mp) cc_final: 0.6479 (mp) REVERT: H 80 LEU cc_start: 0.7629 (tp) cc_final: 0.7052 (tp) REVERT: L 87 TYR cc_start: 0.8498 (m-80) cc_final: 0.8029 (m-80) outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 0.2194 time to fit residues: 33.4516 Evaluate side-chains 103 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 35 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN L 39 GLN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.126247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.101804 restraints weight = 9804.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104669 restraints weight = 5891.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.106632 restraints weight = 4065.854| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 4899 Z= 0.341 Angle : 0.741 8.476 6665 Z= 0.385 Chirality : 0.047 0.176 741 Planarity : 0.006 0.070 860 Dihedral : 6.579 21.493 682 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.35), residues: 621 helix: -2.05 (0.86), residues: 31 sheet: -1.17 (0.34), residues: 226 loop : -1.57 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 353 HIS 0.003 0.001 HIS A 519 PHE 0.010 0.002 PHE H 170 TYR 0.021 0.002 TYR A 453 ARG 0.005 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 355 ARG cc_start: 0.8194 (mmt90) cc_final: 0.7901 (mmt90) REVERT: A 444 LYS cc_start: 0.8240 (ttmt) cc_final: 0.7409 (mmtm) REVERT: A 458 LYS cc_start: 0.8839 (ttmt) cc_final: 0.8353 (tmtt) REVERT: A 465 GLU cc_start: 0.7833 (mt-10) cc_final: 0.7567 (mt-10) REVERT: H 71 ARG cc_start: 0.6227 (mtp85) cc_final: 0.6024 (mtp85) REVERT: H 80 LEU cc_start: 0.7602 (tp) cc_final: 0.7110 (tp) REVERT: H 182 LEU cc_start: 0.9017 (pt) cc_final: 0.8701 (pp) REVERT: L 11 LEU cc_start: 0.8643 (mt) cc_final: 0.8415 (mt) REVERT: L 37 TYR cc_start: 0.8962 (m-80) cc_final: 0.8680 (m-80) REVERT: L 55 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7901 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2213 time to fit residues: 33.7079 Evaluate side-chains 99 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN L 39 GLN L 166 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.131431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.107367 restraints weight = 9747.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.110298 restraints weight = 5812.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.112379 restraints weight = 3987.637| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4899 Z= 0.214 Angle : 0.661 7.947 6665 Z= 0.342 Chirality : 0.047 0.188 741 Planarity : 0.006 0.059 860 Dihedral : 5.938 20.358 682 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.85 (0.35), residues: 621 helix: -1.77 (0.91), residues: 32 sheet: -1.11 (0.32), residues: 240 loop : -1.20 (0.37), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 353 HIS 0.002 0.001 HIS L 198 PHE 0.009 0.001 PHE H 170 TYR 0.014 0.001 TYR L 87 ARG 0.009 0.001 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.8104 (t80) cc_final: 0.7799 (t80) REVERT: A 444 LYS cc_start: 0.8210 (ttmt) cc_final: 0.7436 (mmtm) REVERT: A 458 LYS cc_start: 0.8781 (ttmt) cc_final: 0.8293 (tmtt) REVERT: A 505 TYR cc_start: 0.7919 (m-80) cc_final: 0.7698 (m-80) REVERT: H 88 GLU cc_start: 0.8408 (pm20) cc_final: 0.8111 (pm20) REVERT: L 37 TYR cc_start: 0.8794 (m-80) cc_final: 0.8441 (m-80) REVERT: L 150 VAL cc_start: 0.7964 (t) cc_final: 0.7725 (t) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1913 time to fit residues: 31.3459 Evaluate side-chains 97 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 34 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 3 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 11 optimal weight: 0.0070 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN H 109 GLN H 203 ASN ** L 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.134679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.110563 restraints weight = 9647.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113699 restraints weight = 5631.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115919 restraints weight = 3781.415| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4899 Z= 0.198 Angle : 0.661 11.181 6665 Z= 0.338 Chirality : 0.046 0.184 741 Planarity : 0.005 0.052 860 Dihedral : 5.686 19.999 682 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.19 % Allowed : 4.29 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.54 (0.35), residues: 621 helix: -2.00 (0.82), residues: 32 sheet: -0.73 (0.34), residues: 237 loop : -1.08 (0.37), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 353 HIS 0.001 0.001 HIS A 519 PHE 0.009 0.001 PHE H 126 TYR 0.013 0.001 TYR H 33 ARG 0.004 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 127 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8089 (ttpt) cc_final: 0.7441 (mmtm) REVERT: A 458 LYS cc_start: 0.8794 (ttmt) cc_final: 0.8305 (tmtt) REVERT: H 88 GLU cc_start: 0.8318 (pm20) cc_final: 0.8104 (pm20) REVERT: H 124 SER cc_start: 0.8015 (p) cc_final: 0.7491 (p) REVERT: L 11 LEU cc_start: 0.8374 (mt) cc_final: 0.7958 (mt) REVERT: L 37 TYR cc_start: 0.8856 (m-80) cc_final: 0.8577 (m-80) REVERT: L 150 VAL cc_start: 0.7947 (t) cc_final: 0.7609 (t) outliers start: 1 outliers final: 0 residues processed: 128 average time/residue: 0.1848 time to fit residues: 29.4736 Evaluate side-chains 105 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 24 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 54 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 3 optimal weight: 0.0170 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 overall best weight: 2.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN L 124 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.129170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.104473 restraints weight = 9909.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.107455 restraints weight = 5903.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109537 restraints weight = 4043.364| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.2352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4899 Z= 0.348 Angle : 0.730 7.059 6665 Z= 0.380 Chirality : 0.047 0.215 741 Planarity : 0.006 0.052 860 Dihedral : 6.039 19.904 682 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 0.19 % Allowed : 3.17 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.61 (0.35), residues: 621 helix: -1.87 (0.82), residues: 31 sheet: -0.81 (0.34), residues: 237 loop : -1.13 (0.37), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 353 HIS 0.003 0.001 HIS A 519 PHE 0.016 0.002 PHE H 170 TYR 0.023 0.002 TYR A 453 ARG 0.005 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.539 Fit side-chains revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8450 (pp) cc_final: 0.8101 (tp) REVERT: A 406 GLU cc_start: 0.7880 (mm-30) cc_final: 0.7656 (mm-30) REVERT: A 444 LYS cc_start: 0.8238 (ttpt) cc_final: 0.7418 (mmtm) REVERT: A 458 LYS cc_start: 0.8823 (ttmt) cc_final: 0.8325 (tmtt) REVERT: H 81 GLN cc_start: 0.6703 (tm-30) cc_final: 0.6339 (tt0) REVERT: H 88 GLU cc_start: 0.8473 (pm20) cc_final: 0.8231 (pm20) REVERT: L 11 LEU cc_start: 0.8531 (mt) cc_final: 0.8239 (mt) REVERT: L 37 TYR cc_start: 0.8987 (m-80) cc_final: 0.8683 (m-80) REVERT: L 150 VAL cc_start: 0.8211 (t) cc_final: 0.7930 (t) outliers start: 1 outliers final: 0 residues processed: 133 average time/residue: 0.1816 time to fit residues: 30.1667 Evaluate side-chains 94 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 44 optimal weight: 0.0870 chunk 35 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN H 109 GLN H 203 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.131284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.107211 restraints weight = 9664.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.110182 restraints weight = 5675.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.112175 restraints weight = 3858.635| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4899 Z= 0.218 Angle : 0.665 7.749 6665 Z= 0.343 Chirality : 0.046 0.235 741 Planarity : 0.006 0.051 860 Dihedral : 5.782 18.442 682 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.19 % Allowed : 1.68 % Favored : 98.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.46 (0.35), residues: 621 helix: -2.10 (0.79), residues: 31 sheet: -0.63 (0.34), residues: 234 loop : -1.06 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 353 HIS 0.007 0.001 HIS L 91 PHE 0.011 0.001 PHE H 170 TYR 0.013 0.002 TYR A 453 ARG 0.007 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 134 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8447 (pp) cc_final: 0.8076 (tp) REVERT: A 444 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7409 (mmtm) REVERT: A 458 LYS cc_start: 0.8818 (ttmt) cc_final: 0.8324 (tmtt) REVERT: H 19 ARG cc_start: 0.6612 (ttt180) cc_final: 0.6310 (ttp80) REVERT: H 81 GLN cc_start: 0.6601 (tm-30) cc_final: 0.6224 (tt0) REVERT: H 88 GLU cc_start: 0.8426 (pm20) cc_final: 0.8181 (pm20) REVERT: L 34 LEU cc_start: 0.8802 (tt) cc_final: 0.8544 (tt) REVERT: L 37 TYR cc_start: 0.8879 (m-80) cc_final: 0.8647 (m-80) REVERT: L 72 PHE cc_start: 0.8583 (m-80) cc_final: 0.8377 (m-10) REVERT: L 150 VAL cc_start: 0.8247 (t) cc_final: 0.7932 (t) outliers start: 1 outliers final: 0 residues processed: 135 average time/residue: 0.1887 time to fit residues: 31.3495 Evaluate side-chains 105 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 7.9990 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 9 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN H 109 GLN H 203 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.133834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109631 restraints weight = 9499.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.112624 restraints weight = 5604.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.114708 restraints weight = 3820.179| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4899 Z= 0.195 Angle : 0.658 9.190 6665 Z= 0.337 Chirality : 0.046 0.197 741 Planarity : 0.005 0.053 860 Dihedral : 5.508 18.212 682 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.19 % Allowed : 2.43 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.35), residues: 621 helix: -2.32 (0.75), residues: 32 sheet: -0.54 (0.34), residues: 231 loop : -0.97 (0.36), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 353 HIS 0.005 0.001 HIS L 91 PHE 0.018 0.001 PHE L 139 TYR 0.013 0.001 TYR A 453 ARG 0.010 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.573 Fit side-chains REVERT: A 335 LEU cc_start: 0.8486 (pp) cc_final: 0.8183 (tp) REVERT: A 444 LYS cc_start: 0.8110 (ttpt) cc_final: 0.7402 (mmtm) REVERT: A 458 LYS cc_start: 0.8839 (ttmt) cc_final: 0.8249 (tmtt) REVERT: H 19 ARG cc_start: 0.6452 (ttt180) cc_final: 0.6206 (mtp-110) REVERT: H 81 GLN cc_start: 0.6560 (tm-30) cc_final: 0.6133 (tt0) REVERT: H 88 GLU cc_start: 0.8357 (pm20) cc_final: 0.8132 (pm20) REVERT: H 158 TRP cc_start: 0.7134 (m100) cc_final: 0.6854 (m100) REVERT: L 34 LEU cc_start: 0.8736 (tt) cc_final: 0.8528 (tt) REVERT: L 37 TYR cc_start: 0.8943 (m-80) cc_final: 0.8675 (m-80) REVERT: L 150 VAL cc_start: 0.8226 (t) cc_final: 0.7866 (t) outliers start: 1 outliers final: 1 residues processed: 131 average time/residue: 0.1827 time to fit residues: 29.9123 Evaluate side-chains 98 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 8.9990 chunk 44 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.135343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.110488 restraints weight = 9548.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.113688 restraints weight = 5556.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.115872 restraints weight = 3716.373| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4899 Z= 0.205 Angle : 0.679 8.243 6665 Z= 0.347 Chirality : 0.047 0.242 741 Planarity : 0.006 0.052 860 Dihedral : 5.499 18.594 682 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.27 (0.35), residues: 621 helix: -2.43 (0.73), residues: 32 sheet: -0.42 (0.34), residues: 230 loop : -0.94 (0.36), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.004 0.001 HIS L 91 PHE 0.018 0.002 PHE L 139 TYR 0.014 0.001 TYR A 453 ARG 0.008 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8562 (pp) cc_final: 0.8263 (tp) REVERT: A 444 LYS cc_start: 0.8120 (ttpt) cc_final: 0.7413 (mmtm) REVERT: A 458 LYS cc_start: 0.8857 (ttmt) cc_final: 0.8310 (tmtt) REVERT: H 19 ARG cc_start: 0.6517 (ttt180) cc_final: 0.6282 (mtp85) REVERT: H 81 GLN cc_start: 0.6554 (tm-30) cc_final: 0.6157 (tt0) REVERT: H 88 GLU cc_start: 0.8308 (pm20) cc_final: 0.8089 (pm20) REVERT: H 158 TRP cc_start: 0.6979 (m100) cc_final: 0.6738 (m100) REVERT: L 150 VAL cc_start: 0.8368 (t) cc_final: 0.7936 (t) REVERT: L 207 LYS cc_start: 0.5843 (mmpt) cc_final: 0.5443 (tppt) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1898 time to fit residues: 31.7343 Evaluate side-chains 107 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 7.9990 chunk 4 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 GLN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.129610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.104931 restraints weight = 9662.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.107795 restraints weight = 5779.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.109921 restraints weight = 4001.646| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4899 Z= 0.352 Angle : 0.735 6.869 6665 Z= 0.384 Chirality : 0.048 0.223 741 Planarity : 0.006 0.053 860 Dihedral : 5.888 21.152 682 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.19 % Allowed : 1.12 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 (0.36), residues: 621 helix: -2.41 (0.74), residues: 31 sheet: -0.40 (0.35), residues: 224 loop : -0.99 (0.36), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 353 HIS 0.006 0.002 HIS L 91 PHE 0.019 0.002 PHE L 139 TYR 0.024 0.002 TYR A 453 ARG 0.006 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 135 time to evaluate : 0.574 Fit side-chains revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8550 (pp) cc_final: 0.8249 (tp) REVERT: A 444 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7374 (mmtm) REVERT: A 458 LYS cc_start: 0.8870 (ttmt) cc_final: 0.8344 (tmtt) REVERT: H 19 ARG cc_start: 0.6551 (ttt180) cc_final: 0.6326 (mtp85) REVERT: H 81 GLN cc_start: 0.6649 (tm-30) cc_final: 0.6313 (tt0) REVERT: H 88 GLU cc_start: 0.8464 (pm20) cc_final: 0.8193 (pm20) REVERT: L 150 VAL cc_start: 0.8279 (t) cc_final: 0.7922 (t) REVERT: L 207 LYS cc_start: 0.5910 (mmpt) cc_final: 0.5525 (tppt) outliers start: 1 outliers final: 1 residues processed: 136 average time/residue: 0.1930 time to fit residues: 32.3750 Evaluate side-chains 102 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 201 ASN ** 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 = 0.3727 r_free = 0.3727 target = 0.132568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.107986 restraints weight = 9638.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.110986 restraints weight = 5719.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.113064 restraints weight = 3920.908| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4899 Z= 0.233 Angle : 0.709 7.864 6665 Z= 0.361 Chirality : 0.048 0.286 741 Planarity : 0.006 0.051 860 Dihedral : 5.668 19.304 682 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.28 (0.35), residues: 621 helix: -2.71 (0.71), residues: 32 sheet: -0.35 (0.36), residues: 215 loop : -0.97 (0.35), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 353 HIS 0.005 0.001 HIS L 91 PHE 0.021 0.002 PHE L 139 TYR 0.019 0.001 TYR A 453 ARG 0.009 0.001 ARG L 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1242 Ramachandran restraints generated. 621 Oldfield, 0 Emsley, 621 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8528 (pp) cc_final: 0.8215 (tp) REVERT: A 444 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7406 (mmtm) REVERT: A 458 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8378 (tmtt) REVERT: H 19 ARG cc_start: 0.6353 (ttt180) cc_final: 0.6064 (mtp85) REVERT: H 81 GLN cc_start: 0.6615 (tm-30) cc_final: 0.6302 (tt0) REVERT: H 88 GLU cc_start: 0.8396 (pm20) cc_final: 0.8150 (pm20) REVERT: H 158 TRP cc_start: 0.6866 (m100) cc_final: 0.6498 (m100) REVERT: L 37 TYR cc_start: 0.8978 (m-80) cc_final: 0.8755 (m-80) REVERT: L 150 VAL cc_start: 0.8263 (t) cc_final: 0.7854 (t) REVERT: L 207 LYS cc_start: 0.5817 (mmpt) cc_final: 0.5432 (tppt) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1961 time to fit residues: 33.3076 Evaluate side-chains 105 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 57 optimal weight: 10.0000 chunk 35 optimal weight: 0.0670 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 49 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN A 409 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 GLN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.136176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111554 restraints weight = 9544.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114756 restraints weight = 5556.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116971 restraints weight = 3734.866| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4899 Z= 0.186 Angle : 0.679 9.805 6665 Z= 0.342 Chirality : 0.046 0.203 741 Planarity : 0.005 0.049 860 Dihedral : 5.444 18.343 682 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.19 % Allowed : 0.37 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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 (0.35), residues: 621 helix: -2.85 (0.68), residues: 32 sheet: -0.42 (0.34), residues: 230 loop : -0.81 (0.37), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 353 HIS 0.005 0.001 HIS L 91 PHE 0.019 0.001 PHE L 139 TYR 0.017 0.001 TYR L 50 ARG 0.008 0.001 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1989.23 seconds wall clock time: 35 minutes 12.74 seconds (2112.74 seconds total)