Starting phenix.real_space_refine on Thu Jun 5 01:28:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7swo_25477/06_2025/7swo_25477_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7swo_25477/06_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_25477/06_2025/7swo_25477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7swo_25477/06_2025/7swo_25477.map" model { file = "/net/cci-nas-00/data/ceres_data/7swo_25477/06_2025/7swo_25477_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7swo_25477/06_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-5710/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: 3.17, per 1000 atoms: 0.66 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: 1.03 Conformation dependent library (CDL) restraints added in 517.6 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: 0.51 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: 1.25 Time building geometry restraints manager: 1.22 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: 1.030 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.010 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.490 ------------------------------------------------------------------------------- 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 4907 Z= 0.312 Angle : 0.897 9.655 6681 Z= 0.487 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 Details of bonding type rmsd hydrogen bonds : bond 0.13312 ( 153) hydrogen bonds : angle 9.48945 ( 363) SS BOND : bond 0.00570 ( 8) SS BOND : angle 1.76795 ( 16) covalent geometry : bond 0.00665 ( 4899) covalent geometry : angle 0.89347 ( 6665) *********************** 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 : 0.585 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: 0.2240 time to fit residues: 34.0661 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 : 0.563 ------------------------------------------------------------------------------- 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 4907 Z= 0.229 Angle : 0.744 8.476 6681 Z= 0.386 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 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 153) hydrogen bonds : angle 8.46378 ( 363) SS BOND : bond 0.00462 ( 8) SS BOND : angle 1.46361 ( 16) covalent geometry : bond 0.00516 ( 4899) covalent geometry : angle 0.74119 ( 6665) *********************** 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 : 0.507 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: 0.2171 time to fit residues: 32.9791 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 : 0.555 ------------------------------------------------------------------------------- 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 4907 Z= 0.141 Angle : 0.663 7.947 6681 Z= 0.343 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 Details of bonding type rmsd hydrogen bonds : bond 0.03449 ( 153) hydrogen bonds : angle 7.76239 ( 363) SS BOND : bond 0.00467 ( 8) SS BOND : angle 1.28299 ( 16) covalent geometry : bond 0.00323 ( 4899) covalent geometry : angle 0.66071 ( 6665) *********************** 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 : 0.528 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: 0.1908 time to fit residues: 31.2016 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 : 0.570 ------------------------------------------------------------------------------- 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 4907 Z= 0.128 Angle : 0.662 11.181 6681 Z= 0.339 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 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 153) hydrogen bonds : angle 7.26864 ( 363) SS BOND : bond 0.00446 ( 8) SS BOND : angle 1.10642 ( 16) covalent geometry : bond 0.00294 ( 4899) covalent geometry : angle 0.66077 ( 6665) *********************** 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 : 0.581 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: 0.1996 time to fit residues: 31.7927 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 : 0.611 ------------------------------------------------------------------------------- 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: 6.9990 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: 6.9990 chunk 47 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 overall best weight: 2.3584 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.128638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104122 restraints weight = 9934.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.107063 restraints weight = 5946.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.109095 restraints weight = 4081.788| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4907 Z= 0.242 Angle : 0.741 6.949 6681 Z= 0.386 Chirality : 0.048 0.220 741 Planarity : 0.006 0.052 860 Dihedral : 6.092 20.230 682 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % 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: -1.64 (0.35), residues: 621 helix: -1.86 (0.83), residues: 31 sheet: -0.80 (0.34), residues: 236 loop : -1.18 (0.36), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 353 HIS 0.004 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 Details of bonding type rmsd hydrogen bonds : bond 0.03661 ( 153) hydrogen bonds : angle 7.60852 ( 363) SS BOND : bond 0.00559 ( 8) SS BOND : angle 1.65665 ( 16) covalent geometry : bond 0.00543 ( 4899) covalent geometry : angle 0.73769 ( 6665) *********************** 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 134 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8418 (pp) cc_final: 0.8066 (tp) REVERT: A 444 LYS cc_start: 0.8232 (ttpt) cc_final: 0.7420 (mmtm) REVERT: A 458 LYS cc_start: 0.8814 (ttmt) cc_final: 0.8327 (tmtt) REVERT: H 81 GLN cc_start: 0.6706 (tm-30) cc_final: 0.6349 (tt0) REVERT: H 88 GLU cc_start: 0.8485 (pm20) cc_final: 0.8213 (pm20) REVERT: L 11 LEU cc_start: 0.8539 (mt) cc_final: 0.8252 (mt) REVERT: L 37 TYR cc_start: 0.8991 (m-80) cc_final: 0.8700 (m-80) REVERT: L 150 VAL cc_start: 0.8201 (t) cc_final: 0.7922 (t) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.1927 time to fit residues: 32.0561 Evaluate side-chains 95 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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: 0.7980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3705 r_free = 0.3705 target = 0.131565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.107367 restraints weight = 9674.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.110352 restraints weight = 5672.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.112457 restraints weight = 3837.355| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4907 Z= 0.140 Angle : 0.661 7.824 6681 Z= 0.341 Chirality : 0.046 0.225 741 Planarity : 0.006 0.052 860 Dihedral : 5.741 18.238 682 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.19 % Allowed : 2.05 % Favored : 97.76 % 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: -1.45 (0.35), residues: 621 helix: -2.07 (0.78), residues: 31 sheet: -0.63 (0.34), residues: 234 loop : -1.05 (0.36), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 353 HIS 0.006 0.001 HIS L 91 PHE 0.012 0.001 PHE H 126 TYR 0.012 0.002 TYR H 33 ARG 0.007 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 153) hydrogen bonds : angle 7.20859 ( 363) SS BOND : bond 0.00476 ( 8) SS BOND : angle 1.10820 ( 16) covalent geometry : bond 0.00320 ( 4899) covalent geometry : angle 0.65985 ( 6665) *********************** 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: 1 poor density : 133 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8442 (pp) cc_final: 0.8072 (tp) REVERT: A 444 LYS cc_start: 0.8198 (ttpt) cc_final: 0.7411 (mmtm) REVERT: A 458 LYS cc_start: 0.8813 (ttmt) cc_final: 0.8327 (tmtt) REVERT: H 81 GLN cc_start: 0.6592 (tm-30) cc_final: 0.6223 (tt0) REVERT: H 88 GLU cc_start: 0.8423 (pm20) cc_final: 0.8178 (pm20) REVERT: L 34 LEU cc_start: 0.8811 (tt) cc_final: 0.8524 (tt) REVERT: L 37 TYR cc_start: 0.8874 (m-80) cc_final: 0.8645 (m-80) REVERT: L 72 PHE cc_start: 0.8569 (m-80) cc_final: 0.8339 (m-10) REVERT: L 150 VAL cc_start: 0.8247 (t) cc_final: 0.7930 (t) outliers start: 1 outliers final: 0 residues processed: 134 average time/residue: 0.1901 time to fit residues: 31.5330 Evaluate side-chains 101 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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: 4.9990 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.130749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.106184 restraints weight = 9610.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.109177 restraints weight = 5710.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.111240 restraints weight = 3885.486| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4907 Z= 0.178 Angle : 0.689 8.386 6681 Z= 0.354 Chirality : 0.047 0.228 741 Planarity : 0.006 0.054 860 Dihedral : 5.757 20.299 682 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.19 % Allowed : 2.05 % Favored : 97.76 % 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: -1.45 (0.35), residues: 621 helix: -2.12 (0.75), residues: 31 sheet: -0.52 (0.34), residues: 232 loop : -1.14 (0.36), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 353 HIS 0.005 0.001 HIS L 91 PHE 0.018 0.002 PHE L 139 TYR 0.019 0.002 TYR A 453 ARG 0.007 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 153) hydrogen bonds : angle 7.21205 ( 363) SS BOND : bond 0.00475 ( 8) SS BOND : angle 1.24902 ( 16) covalent geometry : bond 0.00406 ( 4899) covalent geometry : angle 0.68715 ( 6665) *********************** 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 130 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8485 (pp) cc_final: 0.8237 (tp) REVERT: A 444 LYS cc_start: 0.8225 (ttpt) cc_final: 0.7405 (mmtm) REVERT: A 458 LYS cc_start: 0.8824 (ttmt) cc_final: 0.8293 (tmtt) REVERT: H 81 GLN cc_start: 0.6644 (tm-30) cc_final: 0.6334 (tt0) REVERT: H 88 GLU cc_start: 0.8456 (pm20) cc_final: 0.8177 (pm20) REVERT: H 158 TRP cc_start: 0.7120 (m100) cc_final: 0.6778 (m100) REVERT: L 34 LEU cc_start: 0.8792 (tt) cc_final: 0.8580 (tt) REVERT: L 37 TYR cc_start: 0.8995 (m-80) cc_final: 0.8725 (m-80) REVERT: L 72 PHE cc_start: 0.8569 (m-80) cc_final: 0.8355 (m-10) REVERT: L 150 VAL cc_start: 0.8198 (t) cc_final: 0.7889 (t) outliers start: 1 outliers final: 1 residues processed: 130 average time/residue: 0.1810 time to fit residues: 29.2768 Evaluate side-chains 95 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.491 ------------------------------------------------------------------------------- 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: 0.9990 chunk 5 optimal weight: 8.9990 chunk 44 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 35 optimal weight: 8.9990 chunk 52 optimal weight: 0.0570 chunk 51 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 203 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.133811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.109117 restraints weight = 9615.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.112088 restraints weight = 5610.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114297 restraints weight = 3837.052| |-----------------------------------------------------------------------------| r_work (final): 0.3461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4907 Z= 0.130 Angle : 0.668 7.995 6681 Z= 0.340 Chirality : 0.047 0.242 741 Planarity : 0.006 0.055 860 Dihedral : 5.529 18.972 682 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % 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: -1.39 (0.35), residues: 621 helix: -2.14 (0.78), residues: 32 sheet: -0.56 (0.33), residues: 233 loop : -1.01 (0.37), residues: 356 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 0.001 PHE L 139 TYR 0.014 0.001 TYR A 453 ARG 0.008 0.000 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 153) hydrogen bonds : angle 6.97921 ( 363) SS BOND : bond 0.00504 ( 8) SS BOND : angle 1.13971 ( 16) covalent geometry : bond 0.00301 ( 4899) covalent geometry : angle 0.66627 ( 6665) *********************** 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 140 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8565 (pp) cc_final: 0.8223 (tp) REVERT: A 444 LYS cc_start: 0.8115 (ttpt) cc_final: 0.7395 (mmtm) REVERT: A 458 LYS cc_start: 0.8914 (ttmt) cc_final: 0.8346 (tmtt) REVERT: H 81 GLN cc_start: 0.6558 (tm-30) cc_final: 0.6161 (tt0) REVERT: H 88 GLU cc_start: 0.8342 (pm20) cc_final: 0.8116 (pm20) REVERT: L 34 LEU cc_start: 0.8780 (tt) cc_final: 0.8515 (tt) REVERT: L 37 TYR cc_start: 0.8876 (m-80) cc_final: 0.8528 (m-80) REVERT: L 72 PHE cc_start: 0.8514 (m-80) cc_final: 0.8254 (m-10) REVERT: L 150 VAL cc_start: 0.8326 (t) cc_final: 0.7940 (t) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1799 time to fit residues: 31.6564 Evaluate side-chains 101 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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: 0.4980 chunk 23 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 37 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.128757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.104631 restraints weight = 9741.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.107493 restraints weight = 5783.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.109509 restraints weight = 3970.249| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 4907 Z= 0.250 Angle : 0.753 7.600 6681 Z= 0.391 Chirality : 0.048 0.225 741 Planarity : 0.006 0.054 860 Dihedral : 6.036 23.036 682 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.19 % Allowed : 0.56 % 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: -1.34 (0.36), residues: 621 helix: -2.09 (0.79), residues: 31 sheet: -0.38 (0.36), residues: 225 loop : -1.10 (0.36), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP H 158 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 0.007 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03657 ( 153) hydrogen bonds : angle 7.29845 ( 363) SS BOND : bond 0.00567 ( 8) SS BOND : angle 1.72338 ( 16) covalent geometry : bond 0.00566 ( 4899) covalent geometry : angle 0.74921 ( 6665) *********************** 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 129 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 128 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8485 (pp) cc_final: 0.8172 (tp) REVERT: A 444 LYS cc_start: 0.8235 (ttpt) cc_final: 0.7389 (mmtm) REVERT: A 458 LYS cc_start: 0.8888 (ttmt) cc_final: 0.8408 (tmtt) REVERT: H 19 ARG cc_start: 0.7739 (mmm-85) cc_final: 0.6762 (ttt90) REVERT: H 81 GLN cc_start: 0.6649 (tm-30) cc_final: 0.6286 (tt0) REVERT: H 88 GLU cc_start: 0.8512 (pm20) cc_final: 0.8220 (pm20) REVERT: L 34 LEU cc_start: 0.8797 (tt) cc_final: 0.8494 (tt) REVERT: L 72 PHE cc_start: 0.8592 (m-80) cc_final: 0.8365 (m-80) REVERT: L 150 VAL cc_start: 0.8275 (t) cc_final: 0.7960 (t) outliers start: 1 outliers final: 1 residues processed: 129 average time/residue: 0.1995 time to fit residues: 31.7123 Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.529 ------------------------------------------------------------------------------- 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: 0.5980 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 23 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.133683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.109582 restraints weight = 9556.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.112706 restraints weight = 5495.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.114784 restraints weight = 3671.132| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4907 Z= 0.133 Angle : 0.684 7.655 6681 Z= 0.350 Chirality : 0.048 0.296 741 Planarity : 0.006 0.055 860 Dihedral : 5.663 18.762 682 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % 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: -1.34 (0.35), residues: 621 helix: -2.43 (0.71), residues: 32 sheet: -0.45 (0.34), residues: 230 loop : -1.00 (0.36), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 158 HIS 0.003 0.001 HIS L 91 PHE 0.020 0.002 PHE L 139 TYR 0.017 0.001 TYR L 50 ARG 0.009 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03237 ( 153) hydrogen bonds : angle 6.96870 ( 363) SS BOND : bond 0.00570 ( 8) SS BOND : angle 1.38410 ( 16) covalent geometry : bond 0.00310 ( 4899) covalent geometry : angle 0.68187 ( 6665) ********************** 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 146 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.8556 (pp) cc_final: 0.8177 (tp) REVERT: A 353 TRP cc_start: 0.8709 (p-90) cc_final: 0.8487 (p-90) REVERT: A 355 ARG cc_start: 0.8064 (mmt90) cc_final: 0.7826 (mmt90) REVERT: A 444 LYS cc_start: 0.8183 (ttpt) cc_final: 0.7398 (mmtm) REVERT: A 458 LYS cc_start: 0.8858 (ttmt) cc_final: 0.8330 (tmtt) REVERT: A 465 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7565 (mt-10) REVERT: H 81 GLN cc_start: 0.6625 (tm-30) cc_final: 0.6235 (tt0) REVERT: H 88 GLU cc_start: 0.8398 (pm20) cc_final: 0.8136 (pm20) REVERT: L 11 LEU cc_start: 0.8176 (mm) cc_final: 0.7899 (mm) REVERT: L 34 LEU cc_start: 0.8719 (tt) cc_final: 0.8503 (tt) REVERT: L 37 TYR cc_start: 0.8883 (m-80) cc_final: 0.8547 (m-80) REVERT: L 90 GLN cc_start: 0.8743 (pp30) cc_final: 0.8531 (pp30) REVERT: L 150 VAL cc_start: 0.8259 (t) cc_final: 0.7841 (t) REVERT: L 207 LYS cc_start: 0.5764 (mmpt) cc_final: 0.5367 (tppt) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1927 time to fit residues: 34.9664 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 : 0.591 ------------------------------------------------------------------------------- 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: 7.9990 chunk 35 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.132255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.108280 restraints weight = 9687.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.111303 restraints weight = 5649.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.113379 restraints weight = 3831.973| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4907 Z= 0.182 Angle : 0.729 8.054 6681 Z= 0.375 Chirality : 0.047 0.248 741 Planarity : 0.006 0.055 860 Dihedral : 5.680 19.841 682 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % 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: -1.35 (0.35), residues: 621 helix: -2.61 (0.72), residues: 32 sheet: -0.41 (0.35), residues: 222 loop : -1.03 (0.36), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP H 158 HIS 0.002 0.001 HIS L 91 PHE 0.020 0.002 PHE L 139 TYR 0.019 0.002 TYR A 453 ARG 0.008 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 153) hydrogen bonds : angle 7.11813 ( 363) SS BOND : bond 0.00463 ( 8) SS BOND : angle 1.35090 ( 16) covalent geometry : bond 0.00420 ( 4899) covalent geometry : angle 0.72700 ( 6665) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2218.34 seconds wall clock time: 39 minutes 20.34 seconds (2360.34 seconds total)