Starting phenix.real_space_refine on Tue Feb 11 07:57:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7swo_25477/02_2025/7swo_25477_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swo_25477/02_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_25477/02_2025/7swo_25477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swo_25477/02_2025/7swo_25477.map" model { file = "/net/cci-nas-00/data/ceres_data/7swo_25477/02_2025/7swo_25477_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swo_25477/02_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.29, per 1000 atoms: 0.69 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: 1.14 Conformation dependent library (CDL) restraints added in 586.1 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: 0.59 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: 1.22 Time building geometry restraints manager: 1.33 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: 0.690 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: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.050 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.920 ------------------------------------------------------------------------------- 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 : 0.582 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: 0.2196 time to fit residues: 33.4695 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 : 0.531 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.101809 restraints weight = 9804.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.104662 restraints weight = 5882.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.106667 restraints weight = 4067.487| |-----------------------------------------------------------------------------| 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 : 0.542 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: 0.8235 (ttmt) cc_final: 0.7409 (mmtm) REVERT: A 458 LYS cc_start: 0.8837 (ttmt) cc_final: 0.8352 (tmtt) REVERT: A 465 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7567 (mt-10) REVERT: H 71 ARG cc_start: 0.6225 (mtp85) cc_final: 0.6021 (mtp85) REVERT: H 80 LEU cc_start: 0.7600 (tp) cc_final: 0.7108 (tp) REVERT: H 182 LEU cc_start: 0.9018 (pt) cc_final: 0.8704 (pp) REVERT: L 11 LEU cc_start: 0.8643 (mt) cc_final: 0.8415 (mt) REVERT: L 37 TYR cc_start: 0.8963 (m-80) cc_final: 0.8680 (m-80) REVERT: L 55 ARG cc_start: 0.8167 (mtp-110) cc_final: 0.7901 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.2273 time to fit residues: 34.6356 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 : 0.515 ------------------------------------------------------------------------------- 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: 0.8980 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.131485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.107258 restraints weight = 9761.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.110224 restraints weight = 5850.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.112315 restraints weight = 4007.820| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2005 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= 0.213 Angle : 0.660 7.729 6665 Z= 0.342 Chirality : 0.047 0.181 741 Planarity : 0.005 0.058 860 Dihedral : 5.945 20.621 682 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % 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: -1.87 (0.35), residues: 621 helix: -1.78 (0.90), residues: 32 sheet: -1.13 (0.32), residues: 240 loop : -1.21 (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 0.015 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 131 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.8099 (t80) cc_final: 0.7795 (t80) REVERT: A 444 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7437 (mmtm) REVERT: A 458 LYS cc_start: 0.8768 (ttmt) cc_final: 0.8312 (tmtt) REVERT: A 505 TYR cc_start: 0.7916 (m-80) cc_final: 0.7696 (m-80) REVERT: H 88 GLU cc_start: 0.8419 (pm20) cc_final: 0.8120 (pm20) REVERT: L 37 TYR cc_start: 0.8797 (m-80) cc_final: 0.8468 (m-80) REVERT: L 150 VAL cc_start: 0.7959 (t) cc_final: 0.7723 (t) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1971 time to fit residues: 31.8441 Evaluate side-chains 100 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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: 6.9990 chunk 30 optimal weight: 0.0770 chunk 23 optimal weight: 0.0970 chunk 52 optimal weight: 0.0770 chunk 3 optimal weight: 9.9990 chunk 37 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN H 39 GLN H 203 ASN ** 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 = 0.3768 r_free = 0.3768 target = 0.136417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.112516 restraints weight = 9626.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.115723 restraints weight = 5614.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118000 restraints weight = 3747.529| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.2739 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= 0.178 Angle : 0.649 11.032 6665 Z= 0.331 Chirality : 0.046 0.179 741 Planarity : 0.005 0.053 860 Dihedral : 5.601 19.790 682 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % 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: -1.51 (0.35), residues: 621 helix: -1.99 (0.81), residues: 32 sheet: -0.74 (0.33), residues: 237 loop : -1.04 (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 L 198 PHE 0.011 0.001 PHE H 126 TYR 0.013 0.001 TYR H 33 ARG 0.007 0.001 ARG A 509 *********************** 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 127 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 444 LYS cc_start: 0.8064 (ttpt) cc_final: 0.7459 (mmtm) REVERT: H 88 GLU cc_start: 0.8264 (pm20) cc_final: 0.8048 (pm20) REVERT: H 124 SER cc_start: 0.7970 (p) cc_final: 0.7392 (p) REVERT: L 37 TYR cc_start: 0.8828 (m-80) cc_final: 0.8517 (m-80) REVERT: L 150 VAL cc_start: 0.8048 (t) cc_final: 0.7689 (t) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2074 time to fit residues: 32.5077 Evaluate side-chains 106 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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: 0.0470 chunk 41 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 overall best weight: 2.0084 ------------------------------------------------------------------------------- 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 203 ASN L 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.129283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104252 restraints weight = 9880.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.107183 restraints weight = 5943.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.109113 restraints weight = 4109.268| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 4899 Z= 0.325 Angle : 0.720 7.223 6665 Z= 0.374 Chirality : 0.047 0.216 741 Planarity : 0.006 0.050 860 Dihedral : 5.919 19.326 682 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 0.19 % Allowed : 2.61 % Favored : 97.20 % 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: -1.49 (0.36), residues: 621 helix: -1.89 (0.82), residues: 31 sheet: -0.75 (0.34), residues: 238 loop : -1.02 (0.37), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 353 HIS 0.003 0.001 HIS A 519 PHE 0.018 0.002 PHE L 139 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 131 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8457 (pp) cc_final: 0.8136 (tp) REVERT: A 444 LYS cc_start: 0.8247 (ttpt) cc_final: 0.7428 (mmtm) REVERT: A 458 LYS cc_start: 0.8863 (ttmt) cc_final: 0.8442 (tmtt) REVERT: H 11 LEU cc_start: 0.8342 (mp) cc_final: 0.8044 (mp) REVERT: H 81 GLN cc_start: 0.6684 (tm-30) cc_final: 0.6333 (tt0) REVERT: H 88 GLU cc_start: 0.8453 (pm20) cc_final: 0.8240 (pm20) REVERT: L 150 VAL cc_start: 0.8211 (t) cc_final: 0.7888 (t) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1897 time to fit residues: 30.8803 Evaluate side-chains 100 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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: 3.9990 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 35 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 46 optimal weight: 0.0000 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 203 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.132668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.108567 restraints weight = 9615.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.111533 restraints weight = 5626.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.113431 restraints weight = 3820.906| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4899 Z= 0.193 Angle : 0.649 6.947 6665 Z= 0.335 Chirality : 0.046 0.210 741 Planarity : 0.005 0.052 860 Dihedral : 5.614 18.111 682 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % 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: -2.16 (0.76), residues: 32 sheet: -0.59 (0.34), residues: 235 loop : -0.86 (0.37), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 353 HIS 0.006 0.001 HIS L 91 PHE 0.017 0.001 PHE L 139 TYR 0.012 0.001 TYR H 33 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 134 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.559 Fit side-chains revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8497 (pp) cc_final: 0.8109 (tp) REVERT: A 444 LYS cc_start: 0.8122 (ttpt) cc_final: 0.7405 (mmtm) REVERT: A 465 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7648 (mt-10) REVERT: H 19 ARG cc_start: 0.6484 (ttt180) cc_final: 0.6237 (ttp80) REVERT: H 81 GLN cc_start: 0.6532 (tm-30) cc_final: 0.6191 (tt0) REVERT: H 88 GLU cc_start: 0.8356 (pm20) cc_final: 0.8146 (pm20) REVERT: L 34 LEU cc_start: 0.8759 (tt) cc_final: 0.8465 (tt) REVERT: L 150 VAL cc_start: 0.8249 (t) cc_final: 0.7898 (t) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1874 time to fit residues: 31.2991 Evaluate side-chains 100 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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: 10.0000 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 24 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 3 optimal weight: 0.0070 chunk 9 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 1.2602 ------------------------------------------------------------------------------- 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 = 0.3724 r_free = 0.3724 target = 0.132233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.107954 restraints weight = 9530.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.110887 restraints weight = 5623.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.112808 restraints weight = 3851.076| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4899 Z= 0.245 Angle : 0.682 8.852 6665 Z= 0.349 Chirality : 0.047 0.216 741 Planarity : 0.005 0.052 860 Dihedral : 5.623 18.199 682 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: -1.29 (0.36), residues: 621 helix: -2.32 (0.73), residues: 32 sheet: -0.46 (0.34), residues: 230 loop : -0.95 (0.37), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 353 HIS 0.005 0.001 HIS L 91 PHE 0.019 0.002 PHE L 139 TYR 0.017 0.001 TYR A 453 ARG 0.008 0.001 ARG L 24 *********************** 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: 0 poor density : 131 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8512 (pp) cc_final: 0.8249 (tp) REVERT: A 444 LYS cc_start: 0.8175 (ttpt) cc_final: 0.7437 (mmtm) REVERT: H 19 ARG cc_start: 0.6473 (ttt180) cc_final: 0.6197 (mtp-110) REVERT: H 81 GLN cc_start: 0.6582 (tm-30) cc_final: 0.6153 (tt0) REVERT: H 88 GLU cc_start: 0.8380 (pm20) cc_final: 0.8167 (pm20) REVERT: L 103 LYS cc_start: 0.8824 (tttp) cc_final: 0.8529 (tttm) REVERT: L 150 VAL cc_start: 0.8347 (t) cc_final: 0.7970 (t) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1983 time to fit residues: 31.9973 Evaluate side-chains 102 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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: 0.9980 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3726 r_free = 0.3726 target = 0.132392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.108274 restraints weight = 9628.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.111276 restraints weight = 5612.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.113298 restraints weight = 3795.073| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4899 Z= 0.233 Angle : 0.682 7.563 6665 Z= 0.352 Chirality : 0.048 0.262 741 Planarity : 0.005 0.046 860 Dihedral : 5.585 19.286 682 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: -2.47 (0.70), residues: 32 sheet: -0.32 (0.35), residues: 220 loop : -0.92 (0.36), residues: 369 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 0.019 0.002 PHE L 139 TYR 0.017 0.001 TYR A 453 ARG 0.006 0.001 ARG A 355 *********************** 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 132 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8551 (pp) cc_final: 0.8243 (tp) REVERT: A 444 LYS cc_start: 0.8160 (ttpt) cc_final: 0.7429 (mmtm) REVERT: A 458 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8536 (tmtt) REVERT: A 460 ASN cc_start: 0.8290 (t0) cc_final: 0.6606 (m-40) REVERT: H 19 ARG cc_start: 0.6546 (ttt180) cc_final: 0.5993 (ttt90) REVERT: H 81 GLN cc_start: 0.6581 (tm-30) cc_final: 0.6203 (tt0) REVERT: H 158 TRP cc_start: 0.6895 (m100) cc_final: 0.6425 (m100) REVERT: L 103 LYS cc_start: 0.8812 (tttp) cc_final: 0.8547 (tttm) REVERT: L 150 VAL cc_start: 0.8325 (t) cc_final: 0.7925 (t) REVERT: L 207 LYS cc_start: 0.5821 (mmpt) cc_final: 0.5417 (tppt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1994 time to fit residues: 32.6022 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 : 0.536 ------------------------------------------------------------------------------- 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: 8.9990 chunk 4 optimal weight: 0.0010 chunk 23 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 30 optimal weight: 4.9990 overall best weight: 2.7392 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.127322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.103061 restraints weight = 9772.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.105931 restraints weight = 5854.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.107973 restraints weight = 4039.618| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 4899 Z= 0.414 Angle : 0.791 7.356 6665 Z= 0.413 Chirality : 0.049 0.241 741 Planarity : 0.006 0.045 860 Dihedral : 6.220 22.683 682 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % 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: -1.44 (0.35), residues: 621 helix: -2.53 (0.69), residues: 31 sheet: -0.50 (0.36), residues: 223 loop : -1.09 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP H 47 HIS 0.006 0.002 HIS L 91 PHE 0.020 0.002 PHE L 139 TYR 0.027 0.002 TYR A 453 ARG 0.004 0.001 ARG H 71 *********************** 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 131 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.580 Fit side-chains revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8421 (pp) cc_final: 0.8095 (tp) REVERT: A 444 LYS cc_start: 0.8267 (ttpt) cc_final: 0.7374 (mmtp) REVERT: H 19 ARG cc_start: 0.6548 (ttt180) cc_final: 0.6305 (mtp85) REVERT: H 81 GLN cc_start: 0.6736 (tm-30) cc_final: 0.6414 (tt0) REVERT: H 88 GLU cc_start: 0.8448 (pm20) cc_final: 0.8171 (pm20) REVERT: H 158 TRP cc_start: 0.6934 (m100) cc_final: 0.6503 (m100) REVERT: L 103 LYS cc_start: 0.8922 (tttp) cc_final: 0.8531 (tttp) REVERT: L 150 VAL cc_start: 0.8283 (t) cc_final: 0.8002 (t) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1960 time to fit residues: 31.5565 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 : 0.562 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 1 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3723 r_free = 0.3723 target = 0.132478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.108455 restraints weight = 9550.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.111453 restraints weight = 5628.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.113503 restraints weight = 3817.742| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4899 Z= 0.211 Angle : 0.707 7.998 6665 Z= 0.361 Chirality : 0.049 0.315 741 Planarity : 0.005 0.043 860 Dihedral : 5.765 20.226 682 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % 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: -2.71 (0.68), residues: 32 sheet: -0.42 (0.35), residues: 220 loop : -1.02 (0.35), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 353 HIS 0.002 0.001 HIS L 91 PHE 0.021 0.002 PHE L 139 TYR 0.018 0.001 TYR A 453 ARG 0.005 0.001 ARG A 457 ********************** 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 134 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.544 Fit side-chains revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8516 (pp) cc_final: 0.8181 (tp) REVERT: A 444 LYS cc_start: 0.8204 (ttpt) cc_final: 0.7377 (mmtm) REVERT: A 458 LYS cc_start: 0.8719 (ttmt) cc_final: 0.8493 (tppp) REVERT: A 460 ASN cc_start: 0.8067 (t0) cc_final: 0.6769 (m-40) REVERT: A 465 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7672 (mt-10) REVERT: H 19 ARG cc_start: 0.6270 (ttt180) cc_final: 0.5836 (ttt90) REVERT: H 81 GLN cc_start: 0.6619 (tm-30) cc_final: 0.6241 (tt0) REVERT: H 88 GLU cc_start: 0.8310 (pm20) cc_final: 0.8083 (pm20) REVERT: H 154 VAL cc_start: 0.8360 (t) cc_final: 0.8059 (t) REVERT: L 103 LYS cc_start: 0.8822 (tttp) cc_final: 0.8538 (tttp) REVERT: L 150 VAL cc_start: 0.8212 (t) cc_final: 0.7838 (t) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1910 time to fit residues: 31.5028 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 : 0.587 ------------------------------------------------------------------------------- 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: 10.0000 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 109 GLN ** 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 = 0.3708 r_free = 0.3708 target = 0.131237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.106878 restraints weight = 9584.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109760 restraints weight = 5688.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.111890 restraints weight = 3925.686| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4899 Z= 0.267 Angle : 0.715 8.234 6665 Z= 0.370 Chirality : 0.048 0.268 741 Planarity : 0.006 0.042 860 Dihedral : 5.770 22.255 682 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % 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: -1.32 (0.35), residues: 621 helix: -2.52 (0.74), residues: 32 sheet: -0.39 (0.35), residues: 219 loop : -1.01 (0.35), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 353 HIS 0.003 0.001 HIS H 204 PHE 0.020 0.002 PHE L 139 TYR 0.018 0.002 TYR A 453 ARG 0.004 0.001 ARG A 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1944.20 seconds wall clock time: 35 minutes 34.52 seconds (2134.52 seconds total)