Starting phenix.real_space_refine on Mon Sep 23 22:02:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekd_28199/09_2024/8ekd_28199.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekd_28199/09_2024/8ekd_28199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekd_28199/09_2024/8ekd_28199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekd_28199/09_2024/8ekd_28199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekd_28199/09_2024/8ekd_28199.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ekd_28199/09_2024/8ekd_28199.cif" } resolution = 3.6 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= 0.003 sd= 0.278 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3152 atoms to isotropic. 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 13 5.16 5 C 2075 2.51 5 N 540 2.21 5 O 611 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3239 Number of models: 1 Model: "" Number of chains: 4 Chain: "E" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 968 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 857 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 105} Chain: "G" Number of atoms: 1400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1400 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 10, 'TRANS': 163} Chain breaks: 2 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.59, per 1000 atoms: 0.80 Number of scatterers: 3239 At special positions: 0 Unit cell: (94.462, 60.818, 80.228, 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 13 16.00 O 611 8.00 N 540 7.00 C 2075 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 98 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG G 601 " - " ASN G 343 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 393.3 milliseconds 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 7 sheets defined 6.6% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'E' and resid 64 through 67 Processing helix chain 'G' and resid 337 through 343 Processing helix chain 'G' and resid 365 through 371 removed outlier: 3.907A pdb=" N TYR G 369 " --> pdb=" O TYR G 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 407 No H-bonds generated for 'chain 'G' and resid 405 through 407' Processing helix chain 'G' and resid 416 through 421 removed outlier: 3.549A pdb=" N TYR G 421 " --> pdb=" O ASN G 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.506A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER E 7 " --> pdb=" O SER E 21 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR E 82 " --> pdb=" O SER E 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'E' and resid 60 through 62 removed outlier: 7.212A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.506A pdb=" N ASN F 22 " --> pdb=" O SER F 7 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.644A pdb=" N GLU F 110 " --> pdb=" O LEU F 11 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU F 39 " --> pdb=" O TYR F 55 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR F 55 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TRP F 41 " --> pdb=" O LEU F 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 354 through 356 removed outlier: 3.503A pdb=" N TYR G 396 " --> pdb=" O SER G 514 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP G 398 " --> pdb=" O VAL G 512 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 452 through 454 71 hydrogen bonds defined for protein. 189 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: 0.81 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 893 1.33 - 1.45: 677 1.45 - 1.57: 1735 1.57 - 1.69: 1 1.69 - 1.81: 17 Bond restraints: 3323 Sorted by residual: bond pdb=" N GLN G 474 " pdb=" CA GLN G 474 " ideal model delta sigma weight residual 1.456 1.489 -0.034 1.22e-02 6.72e+03 7.66e+00 bond pdb=" CB PRO G 507 " pdb=" CG PRO G 507 " ideal model delta sigma weight residual 1.492 1.630 -0.138 5.00e-02 4.00e+02 7.65e+00 bond pdb=" CA SER G 459 " pdb=" CB SER G 459 " ideal model delta sigma weight residual 1.527 1.487 0.040 1.44e-02 4.82e+03 7.58e+00 bond pdb=" N LYS G 458 " pdb=" CA LYS G 458 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.21e-02 6.83e+03 7.41e+00 bond pdb=" N TYR G 473 " pdb=" CA TYR G 473 " ideal model delta sigma weight residual 1.457 1.488 -0.032 1.31e-02 5.83e+03 5.91e+00 ... (remaining 3318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 4357 2.23 - 4.46: 121 4.46 - 6.69: 19 6.69 - 8.91: 7 8.91 - 11.14: 2 Bond angle restraints: 4506 Sorted by residual: angle pdb=" N GLN G 474 " pdb=" CA GLN G 474 " pdb=" C GLN G 474 " ideal model delta sigma weight residual 110.28 121.42 -11.14 1.48e+00 4.57e-01 5.67e+01 angle pdb=" CA PRO G 507 " pdb=" N PRO G 507 " pdb=" CD PRO G 507 " ideal model delta sigma weight residual 112.00 103.04 8.96 1.40e+00 5.10e-01 4.09e+01 angle pdb=" C THR G 470 " pdb=" CA THR G 470 " pdb=" CB THR G 470 " ideal model delta sigma weight residual 111.22 103.83 7.39 1.23e+00 6.61e-01 3.61e+01 angle pdb=" CA ALA G 475 " pdb=" C ALA G 475 " pdb=" N GLY G 476 " ideal model delta sigma weight residual 119.63 114.99 4.64 8.10e-01 1.52e+00 3.28e+01 angle pdb=" C SER G 459 " pdb=" N ASN G 460 " pdb=" CA ASN G 460 " ideal model delta sigma weight residual 120.82 112.85 7.97 1.41e+00 5.03e-01 3.19e+01 ... (remaining 4501 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.36: 1670 21.36 - 42.72: 236 42.72 - 64.07: 26 64.07 - 85.43: 9 85.43 - 106.79: 8 Dihedral angle restraints: 1949 sinusoidal: 769 harmonic: 1180 Sorted by residual: dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 98 " pdb=" CB CYS E 98 " ideal model delta sinusoidal sigma weight residual 93.00 44.64 48.36 1 1.00e+01 1.00e-02 3.22e+01 dihedral pdb=" CA PRO F 65 " pdb=" C PRO F 65 " pdb=" N ASP F 66 " pdb=" CA ASP F 66 " ideal model delta harmonic sigma weight residual -180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" C2 NAG G 601 " pdb=" C3 NAG G 601 " pdb=" C4 NAG G 601 " pdb=" O4 NAG G 601 " ideal model delta sinusoidal sigma weight residual 175.11 68.32 106.79 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 1946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 356 0.045 - 0.091: 83 0.091 - 0.136: 25 0.136 - 0.182: 3 0.182 - 0.227: 6 Chirality restraints: 473 Sorted by residual: chirality pdb=" CB ILE E 51 " pdb=" CA ILE E 51 " pdb=" CG1 ILE E 51 " pdb=" CG2 ILE E 51 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA THR G 470 " pdb=" N THR G 470 " pdb=" C THR G 470 " pdb=" CB THR G 470 " both_signs ideal model delta sigma weight residual False 2.53 2.75 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA ARG G 457 " pdb=" N ARG G 457 " pdb=" C ARG G 457 " pdb=" CB ARG G 457 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.19 2.00e-01 2.50e+01 9.50e-01 ... (remaining 470 not shown) Planarity restraints: 581 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER G 383 " -0.079 5.00e-02 4.00e+02 1.17e-01 2.18e+01 pdb=" N PRO G 384 " 0.202 5.00e-02 4.00e+02 pdb=" CA PRO G 384 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO G 384 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN F 48 " -0.054 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO F 49 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO F 49 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO F 49 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 471 " -0.015 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C GLU G 471 " 0.055 2.00e-02 2.50e+03 pdb=" O GLU G 471 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE G 472 " -0.019 2.00e-02 2.50e+03 ... (remaining 578 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 256 2.73 - 3.27: 3328 3.27 - 3.82: 5704 3.82 - 4.36: 6739 4.36 - 4.90: 11108 Nonbonded interactions: 27135 Sorted by model distance: nonbonded pdb=" O PRO F 8 " pdb=" OG1 THR F 107 " model vdw 2.190 3.040 nonbonded pdb=" O PRO G 479 " pdb=" SG CYS G 480 " model vdw 2.195 3.400 nonbonded pdb=" OH TYR E 106 " pdb=" O TYR F 97 " model vdw 2.203 3.040 nonbonded pdb=" OE1 GLU G 406 " pdb=" NE2 GLN G 409 " model vdw 2.205 3.120 nonbonded pdb=" O GLY E 116 " pdb=" OG SER F 62 " model vdw 2.239 3.040 ... (remaining 27130 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: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.780 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 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 : 0.005 0.138 3323 Z= 0.334 Angle : 0.883 11.143 4506 Z= 0.531 Chirality : 0.049 0.227 473 Planarity : 0.009 0.117 580 Dihedral : 19.664 106.791 1196 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.77 % Allowed : 38.94 % Favored : 59.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.67 (0.40), residues: 399 helix: -0.53 (1.97), residues: 7 sheet: -1.25 (0.46), residues: 120 loop : -1.07 (0.37), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP E 121 HIS 0.002 0.001 HIS G 505 PHE 0.008 0.001 PHE E 118 TYR 0.017 0.002 TYR E 105 ARG 0.009 0.001 ARG F 60 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 112 GLU cc_start: 0.5854 (pm20) cc_final: 0.5353 (pm20) outliers start: 6 outliers final: 5 residues processed: 100 average time/residue: 0.1796 time to fit residues: 21.2187 Evaluate side-chains 102 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 97 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain G residue 357 ARG Chi-restraints excluded: chain G residue 456 PHE Chi-restraints excluded: chain G residue 457 ARG Chi-restraints excluded: chain G residue 459 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.0870 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.0000 chunk 31 optimal weight: 0.5980 chunk 12 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.4964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3323 Z= 0.211 Angle : 0.674 7.169 4506 Z= 0.345 Chirality : 0.046 0.252 473 Planarity : 0.007 0.075 580 Dihedral : 8.949 56.402 489 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 5.90 % Allowed : 30.09 % Favored : 64.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.62 (0.40), residues: 399 helix: -0.49 (1.97), residues: 7 sheet: -1.32 (0.47), residues: 113 loop : -0.99 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 121 HIS 0.000 0.000 HIS G 505 PHE 0.007 0.001 PHE G 497 TYR 0.014 0.002 TYR E 105 ARG 0.004 0.001 ARG F 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 TYR cc_start: 0.4643 (OUTLIER) cc_final: 0.3606 (m-80) REVERT: E 112 GLU cc_start: 0.5687 (pm20) cc_final: 0.5310 (pm20) REVERT: F 67 ARG cc_start: 0.5628 (ptt-90) cc_final: 0.5052 (ptt-90) REVERT: G 406 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.6851 (mm-30) REVERT: G 429 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7193 (p90) REVERT: G 459 SER cc_start: 0.8416 (t) cc_final: 0.7829 (p) outliers start: 20 outliers final: 9 residues processed: 110 average time/residue: 0.1598 time to fit residues: 21.0296 Evaluate side-chains 105 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 429 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 85 GLN F 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3323 Z= 0.267 Angle : 0.670 6.096 4506 Z= 0.342 Chirality : 0.046 0.284 473 Planarity : 0.006 0.061 580 Dihedral : 6.234 53.680 476 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 6.78 % Allowed : 31.27 % Favored : 61.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.40), residues: 399 helix: -0.35 (1.96), residues: 7 sheet: -0.88 (0.48), residues: 115 loop : -1.05 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 121 HIS 0.001 0.000 HIS G 505 PHE 0.026 0.002 PHE E 118 TYR 0.013 0.002 TYR E 105 ARG 0.002 0.000 ARG E 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 TYR cc_start: 0.4815 (OUTLIER) cc_final: 0.3854 (m-80) REVERT: E 112 GLU cc_start: 0.5777 (pm20) cc_final: 0.5383 (pm20) REVERT: F 59 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6467 (tm-30) REVERT: F 60 ARG cc_start: 0.5813 (ttm-80) cc_final: 0.5240 (tpp80) REVERT: F 67 ARG cc_start: 0.5984 (ptt-90) cc_final: 0.5580 (ptt-90) REVERT: G 398 ASP cc_start: 0.8105 (m-30) cc_final: 0.6763 (m-30) REVERT: G 406 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7145 (mm-30) REVERT: G 409 GLN cc_start: 0.6937 (mt0) cc_final: 0.6427 (tt0) REVERT: G 429 PHE cc_start: 0.7483 (OUTLIER) cc_final: 0.6755 (p90) REVERT: G 457 ARG cc_start: 0.7680 (ptm-80) cc_final: 0.7448 (ptm-80) REVERT: G 459 SER cc_start: 0.8357 (t) cc_final: 0.7910 (p) outliers start: 23 outliers final: 11 residues processed: 115 average time/residue: 0.1664 time to fit residues: 22.6982 Evaluate side-chains 112 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 429 PHE Chi-restraints excluded: chain G residue 473 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 0.0470 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 123 GLN F 85 GLN ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3323 Z= 0.196 Angle : 0.635 6.177 4506 Z= 0.324 Chirality : 0.044 0.188 473 Planarity : 0.006 0.060 580 Dihedral : 5.480 38.448 476 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 7.08 % Allowed : 31.86 % Favored : 61.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.41), residues: 399 helix: -0.30 (1.99), residues: 7 sheet: -0.67 (0.50), residues: 115 loop : -1.04 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 121 HIS 0.000 0.000 HIS G 505 PHE 0.021 0.001 PHE E 118 TYR 0.013 0.002 TYR E 105 ARG 0.002 0.000 ARG E 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 103 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 112 GLU cc_start: 0.5647 (pm20) cc_final: 0.5255 (pm20) REVERT: F 67 ARG cc_start: 0.5915 (ptt-90) cc_final: 0.5484 (ptt-90) REVERT: G 398 ASP cc_start: 0.8071 (m-30) cc_final: 0.7630 (m-30) REVERT: G 406 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7191 (mm-30) REVERT: G 409 GLN cc_start: 0.6864 (mt0) cc_final: 0.6373 (tt0) REVERT: G 429 PHE cc_start: 0.7368 (OUTLIER) cc_final: 0.6856 (p90) REVERT: G 462 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7253 (mmtt) REVERT: G 495 TYR cc_start: 0.4581 (OUTLIER) cc_final: 0.4158 (m-80) outliers start: 24 outliers final: 11 residues processed: 118 average time/residue: 0.1762 time to fit residues: 24.6370 Evaluate side-chains 109 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 28 SER Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 429 PHE Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 473 TYR Chi-restraints excluded: chain G residue 495 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6414 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3323 Z= 0.409 Angle : 0.768 8.055 4506 Z= 0.392 Chirality : 0.046 0.219 473 Planarity : 0.007 0.062 580 Dihedral : 5.964 37.720 476 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 8.26 % Allowed : 31.27 % Favored : 60.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.41), residues: 399 helix: -0.58 (1.75), residues: 7 sheet: -0.72 (0.50), residues: 115 loop : -1.16 (0.36), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP E 121 HIS 0.001 0.001 HIS G 505 PHE 0.024 0.002 PHE E 118 TYR 0.016 0.003 TYR E 106 ARG 0.003 0.001 ARG G 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 TYR cc_start: 0.4819 (OUTLIER) cc_final: 0.3904 (m-80) REVERT: E 112 GLU cc_start: 0.5950 (pm20) cc_final: 0.5489 (pm20) REVERT: F 67 ARG cc_start: 0.5969 (ptt-90) cc_final: 0.5526 (ptt-90) REVERT: G 356 LYS cc_start: 0.8197 (mptt) cc_final: 0.7943 (mptt) REVERT: G 398 ASP cc_start: 0.8205 (m-30) cc_final: 0.7604 (m-30) REVERT: G 406 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7140 (mm-30) REVERT: G 409 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.6554 (tt0) REVERT: G 429 PHE cc_start: 0.7631 (OUTLIER) cc_final: 0.6677 (p90) REVERT: G 495 TYR cc_start: 0.4555 (OUTLIER) cc_final: 0.3897 (m-80) REVERT: G 501 TYR cc_start: 0.6663 (OUTLIER) cc_final: 0.6254 (m-10) outliers start: 28 outliers final: 15 residues processed: 119 average time/residue: 0.1738 time to fit residues: 24.3388 Evaluate side-chains 117 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 30 ARG Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 369 TYR Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 429 PHE Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 462 LYS Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain G residue 501 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 0.0770 chunk 37 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.2475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3323 Z= 0.202 Angle : 0.671 8.473 4506 Z= 0.337 Chirality : 0.044 0.190 473 Planarity : 0.006 0.059 580 Dihedral : 5.385 33.373 476 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 6.78 % Allowed : 31.27 % Favored : 61.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.41), residues: 399 helix: -0.60 (1.84), residues: 7 sheet: -0.61 (0.49), residues: 115 loop : -1.05 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 121 HIS 0.001 0.000 HIS G 505 PHE 0.016 0.001 PHE E 118 TYR 0.014 0.002 TYR E 120 ARG 0.004 0.000 ARG F 60 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 101 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 59 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6543 (tm-30) REVERT: F 60 ARG cc_start: 0.5979 (ttm-80) cc_final: 0.5454 (tpp80) REVERT: G 371 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.5568 (p90) REVERT: G 398 ASP cc_start: 0.7974 (m-30) cc_final: 0.7454 (m-30) REVERT: G 406 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7323 (mm-30) REVERT: G 409 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6495 (tt0) REVERT: G 429 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.6929 (p90) REVERT: G 495 TYR cc_start: 0.4273 (OUTLIER) cc_final: 0.3966 (m-80) outliers start: 23 outliers final: 12 residues processed: 118 average time/residue: 0.1645 time to fit residues: 23.0576 Evaluate side-chains 115 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 98 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 101 LEU Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 369 TYR Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 410 ILE Chi-restraints excluded: chain G residue 429 PHE Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 473 TYR Chi-restraints excluded: chain G residue 495 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 19 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: ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6371 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 3323 Z= 0.339 Angle : 0.756 9.234 4506 Z= 0.378 Chirality : 0.046 0.267 473 Planarity : 0.006 0.063 580 Dihedral : 5.625 32.461 476 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 7.96 % Allowed : 30.38 % Favored : 61.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.41), residues: 399 helix: -0.50 (1.81), residues: 7 sheet: -0.61 (0.49), residues: 115 loop : -1.10 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 121 HIS 0.001 0.001 HIS G 505 PHE 0.016 0.002 PHE E 118 TYR 0.016 0.002 TYR G 449 ARG 0.002 0.000 ARG E 50 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 102 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 TYR cc_start: 0.4739 (OUTLIER) cc_final: 0.3836 (m-80) REVERT: F 60 ARG cc_start: 0.5941 (ttm-80) cc_final: 0.5623 (tpp80) REVERT: G 371 PHE cc_start: 0.6680 (OUTLIER) cc_final: 0.5541 (p90) REVERT: G 398 ASP cc_start: 0.8235 (m-30) cc_final: 0.7336 (m-30) REVERT: G 406 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7240 (mm-30) REVERT: G 409 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6459 (tt0) REVERT: G 429 PHE cc_start: 0.7615 (OUTLIER) cc_final: 0.6738 (p90) REVERT: G 495 TYR cc_start: 0.4522 (OUTLIER) cc_final: 0.3859 (m-80) outliers start: 27 outliers final: 14 residues processed: 118 average time/residue: 0.1640 time to fit residues: 22.9869 Evaluate side-chains 119 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 82 TYR Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 369 TYR Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 401 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 429 PHE Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 473 TYR Chi-restraints excluded: chain G residue 495 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 3323 Z= 0.240 Angle : 0.722 9.189 4506 Z= 0.357 Chirality : 0.044 0.235 473 Planarity : 0.006 0.063 580 Dihedral : 5.407 30.711 476 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 7.37 % Allowed : 30.38 % Favored : 62.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.41), residues: 399 helix: -0.38 (1.91), residues: 7 sheet: -0.51 (0.49), residues: 115 loop : -1.11 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 121 HIS 0.000 0.000 HIS G 505 PHE 0.015 0.001 PHE E 118 TYR 0.014 0.002 TYR E 120 ARG 0.003 0.000 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 60 ARG cc_start: 0.6044 (ttm-80) cc_final: 0.5698 (tpp80) REVERT: G 371 PHE cc_start: 0.6682 (OUTLIER) cc_final: 0.5558 (p90) REVERT: G 398 ASP cc_start: 0.8140 (m-30) cc_final: 0.7590 (m-30) REVERT: G 406 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: G 409 GLN cc_start: 0.6935 (OUTLIER) cc_final: 0.6453 (tt0) REVERT: G 429 PHE cc_start: 0.7574 (OUTLIER) cc_final: 0.6807 (p90) REVERT: G 495 TYR cc_start: 0.4510 (OUTLIER) cc_final: 0.3996 (m-80) REVERT: G 501 TYR cc_start: 0.6518 (OUTLIER) cc_final: 0.6034 (m-10) outliers start: 25 outliers final: 15 residues processed: 114 average time/residue: 0.1653 time to fit residues: 22.3591 Evaluate side-chains 117 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 369 TYR Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 429 PHE Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 473 TYR Chi-restraints excluded: chain G residue 480 CYS Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain G residue 501 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 18 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.1980 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3323 Z= 0.213 Angle : 0.713 9.181 4506 Z= 0.350 Chirality : 0.044 0.237 473 Planarity : 0.006 0.064 580 Dihedral : 5.170 27.052 476 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 6.78 % Allowed : 31.56 % Favored : 61.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.41), residues: 399 helix: -0.56 (1.82), residues: 7 sheet: -0.40 (0.49), residues: 115 loop : -1.09 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 121 HIS 0.000 0.000 HIS G 505 PHE 0.015 0.001 PHE E 118 TYR 0.012 0.002 TYR E 120 ARG 0.003 0.000 ARG G 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 96 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 20 THR cc_start: 0.7538 (OUTLIER) cc_final: 0.7093 (p) REVERT: F 60 ARG cc_start: 0.5994 (ttm-80) cc_final: 0.5756 (tpp80) REVERT: G 357 ARG cc_start: 0.7503 (tmm-80) cc_final: 0.6620 (tmm160) REVERT: G 371 PHE cc_start: 0.6656 (OUTLIER) cc_final: 0.5532 (p90) REVERT: G 398 ASP cc_start: 0.8075 (m-30) cc_final: 0.7510 (m-30) REVERT: G 406 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7245 (mm-30) REVERT: G 409 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6432 (tt0) REVERT: G 429 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.6648 (p90) REVERT: G 495 TYR cc_start: 0.4271 (OUTLIER) cc_final: 0.3966 (m-80) REVERT: G 501 TYR cc_start: 0.6478 (OUTLIER) cc_final: 0.5978 (m-10) outliers start: 23 outliers final: 14 residues processed: 113 average time/residue: 0.1903 time to fit residues: 25.4995 Evaluate side-chains 113 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 369 TYR Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 429 PHE Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 473 TYR Chi-restraints excluded: chain G residue 480 CYS Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain G residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 32 optimal weight: 0.0270 chunk 5 optimal weight: 0.0770 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 10.0000 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6283 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3323 Z= 0.236 Angle : 0.735 9.733 4506 Z= 0.360 Chirality : 0.044 0.246 473 Planarity : 0.006 0.066 580 Dihedral : 5.120 25.154 476 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 6.49 % Allowed : 30.68 % Favored : 62.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.41), residues: 399 helix: -0.43 (1.86), residues: 7 sheet: -0.34 (0.49), residues: 115 loop : -1.12 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 121 HIS 0.000 0.000 HIS G 505 PHE 0.014 0.001 PHE E 118 TYR 0.017 0.002 TYR G 380 ARG 0.002 0.000 ARG G 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 798 Ramachandran restraints generated. 399 Oldfield, 0 Emsley, 399 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 94 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 20 THR cc_start: 0.7527 (OUTLIER) cc_final: 0.7086 (p) REVERT: F 60 ARG cc_start: 0.6065 (ttm-80) cc_final: 0.5766 (tpp80) REVERT: G 357 ARG cc_start: 0.7478 (tmm-80) cc_final: 0.6666 (tmm160) REVERT: G 371 PHE cc_start: 0.6652 (OUTLIER) cc_final: 0.5518 (p90) REVERT: G 398 ASP cc_start: 0.8148 (m-30) cc_final: 0.7596 (m-30) REVERT: G 406 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7258 (mm-30) REVERT: G 409 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6418 (tt0) REVERT: G 429 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.6622 (p90) REVERT: G 495 TYR cc_start: 0.4324 (OUTLIER) cc_final: 0.4007 (m-80) REVERT: G 501 TYR cc_start: 0.6501 (OUTLIER) cc_final: 0.6017 (m-10) outliers start: 22 outliers final: 14 residues processed: 110 average time/residue: 0.1688 time to fit residues: 21.9929 Evaluate side-chains 114 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 93 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 86 ASN Chi-restraints excluded: chain E residue 105 TYR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 109 VAL Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain G residue 369 TYR Chi-restraints excluded: chain G residue 371 PHE Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 403 ARG Chi-restraints excluded: chain G residue 406 GLU Chi-restraints excluded: chain G residue 409 GLN Chi-restraints excluded: chain G residue 429 PHE Chi-restraints excluded: chain G residue 434 ILE Chi-restraints excluded: chain G residue 473 TYR Chi-restraints excluded: chain G residue 480 CYS Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain G residue 501 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 1 optimal weight: 30.0000 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 GLN ** 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 = 0.4131 r_free = 0.4131 target = 0.188312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.158552 restraints weight = 4152.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.163541 restraints weight = 2171.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.166976 restraints weight = 1464.348| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3323 Z= 0.219 Angle : 0.736 9.613 4506 Z= 0.362 Chirality : 0.045 0.246 473 Planarity : 0.006 0.065 580 Dihedral : 5.040 26.971 476 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 6.78 % Allowed : 30.68 % Favored : 62.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -1.24 (0.41), residues: 399 helix: -0.34 (1.88), residues: 7 sheet: -0.34 (0.48), residues: 117 loop : -1.09 (0.37), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E 121 HIS 0.000 0.000 HIS G 505 PHE 0.014 0.001 PHE E 118 TYR 0.015 0.002 TYR G 473 ARG 0.003 0.000 ARG F 60 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1214.45 seconds wall clock time: 22 minutes 9.84 seconds (1329.84 seconds total)