Starting phenix.real_space_refine on Thu Jul 18 19:19:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qtd_18649/07_2024/8qtd_18649.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qtd_18649/07_2024/8qtd_18649.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/8qtd_18649/07_2024/8qtd_18649.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qtd_18649/07_2024/8qtd_18649.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qtd_18649/07_2024/8qtd_18649.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qtd_18649/07_2024/8qtd_18649.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= -0.000 sd= 0.016 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 16 5.16 5 C 2058 2.51 5 N 541 2.21 5 O 604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 470": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3219 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1566 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 13, 'TRANS': 181} Chain: "H" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1021 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain: "L" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 632 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 83} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 3.93, per 1000 atoms: 1.22 Number of scatterers: 3219 At special positions: 0 Unit cell: (70.8391, 58.424, 97.8602, 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 16 16.00 O 604 8.00 N 541 7.00 C 2058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 521 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 1.11 Conformation dependent library (CDL) restraints added in 596.9 milliseconds 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 10 sheets defined 13.1% alpha, 37.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 334 through 339 removed outlier: 4.331A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.896A pdb=" N ALA A 369 " --> pdb=" O LEU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 387 removed outlier: 4.951A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 387 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 3.854A pdb=" N SER A 405 " --> pdb=" O ASN A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.785A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 110 removed outlier: 3.802A pdb=" N GLY H 108 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR H 109 " --> pdb=" O SER H 106 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TYR H 110 " --> pdb=" O ALA H 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 105 through 110' Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 359 removed outlier: 7.322A pdb=" N CYS A 358 " --> pdb=" O CYS A 521 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA4, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.827A pdb=" N SER H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP H 73 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.381A pdb=" N GLY H 10 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER H 33 " --> pdb=" O VAL H 99 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.381A pdb=" N GLY H 10 " --> pdb=" O THR H 128 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N CYS H 96 " --> pdb=" O TRP H 121 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N TRP H 121 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N ARG H 98 " --> pdb=" O ASP H 119 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.452A pdb=" N VAL L 10 " --> pdb=" O THR L 107 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.452A pdb=" N VAL L 10 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL L 99 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR L 94 " --> pdb=" O VAL L 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 18 through 23 108 hydrogen bonds defined for protein. 237 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: 0.87 Time building geometry restraints manager: 1.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1016 1.34 - 1.46: 888 1.46 - 1.58: 1386 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3310 Sorted by residual: bond pdb=" C GLY L 12 " pdb=" N SER L 13 " ideal model delta sigma weight residual 1.330 1.348 -0.018 1.47e-02 4.63e+03 1.49e+00 bond pdb=" N LYS H 65 " pdb=" CA LYS H 65 " ideal model delta sigma weight residual 1.457 1.470 -0.013 1.29e-02 6.01e+03 9.79e-01 bond pdb=" C THR A 412 " pdb=" N GLY A 413 " ideal model delta sigma weight residual 1.331 1.319 0.011 1.46e-02 4.69e+03 5.78e-01 bond pdb=" CA VAL A 379 " pdb=" CB VAL A 379 " ideal model delta sigma weight residual 1.540 1.550 -0.010 1.36e-02 5.41e+03 4.96e-01 bond pdb=" CA LYS A 478 " pdb=" CB LYS A 478 " ideal model delta sigma weight residual 1.530 1.542 -0.011 1.69e-02 3.50e+03 4.57e-01 ... (remaining 3305 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.01: 99 107.01 - 113.75: 1708 113.75 - 120.49: 1240 120.49 - 127.24: 1407 127.24 - 133.98: 40 Bond angle restraints: 4494 Sorted by residual: angle pdb=" C GLY L 12 " pdb=" N SER L 13 " pdb=" CA SER L 13 " ideal model delta sigma weight residual 120.68 124.94 -4.26 1.52e+00 4.33e-01 7.87e+00 angle pdb=" C LYS H 65 " pdb=" CA LYS H 65 " pdb=" CB LYS H 65 " ideal model delta sigma weight residual 110.42 115.55 -5.13 1.99e+00 2.53e-01 6.64e+00 angle pdb=" N ASN L 33 " pdb=" CA ASN L 33 " pdb=" C ASN L 33 " ideal model delta sigma weight residual 114.56 111.40 3.16 1.27e+00 6.20e-01 6.19e+00 angle pdb=" CA LYS A 478 " pdb=" CB LYS A 478 " pdb=" CG LYS A 478 " ideal model delta sigma weight residual 114.10 117.99 -3.89 2.00e+00 2.50e-01 3.79e+00 angle pdb=" C CYS A 477 " pdb=" N LYS A 478 " pdb=" CA LYS A 478 " ideal model delta sigma weight residual 121.54 125.24 -3.70 1.91e+00 2.74e-01 3.76e+00 ... (remaining 4489 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.94: 1750 11.94 - 23.87: 119 23.87 - 35.81: 41 35.81 - 47.74: 6 47.74 - 59.68: 3 Dihedral angle restraints: 1919 sinusoidal: 733 harmonic: 1186 Sorted by residual: dihedral pdb=" CA ARG H 112 " pdb=" CB ARG H 112 " pdb=" CG ARG H 112 " pdb=" CD ARG H 112 " ideal model delta sinusoidal sigma weight residual 180.00 127.06 52.94 3 1.50e+01 4.44e-03 9.16e+00 dihedral pdb=" N TYR H 104 " pdb=" CA TYR H 104 " pdb=" CB TYR H 104 " pdb=" CG TYR H 104 " ideal model delta sinusoidal sigma weight residual -60.00 -112.60 52.60 3 1.50e+01 4.44e-03 9.13e+00 dihedral pdb=" N MET H 83 " pdb=" CA MET H 83 " pdb=" CB MET H 83 " pdb=" CG MET H 83 " ideal model delta sinusoidal sigma weight residual -180.00 -132.62 -47.38 3 1.50e+01 4.44e-03 8.48e+00 ... (remaining 1916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 256 0.027 - 0.053: 137 0.053 - 0.080: 34 0.080 - 0.106: 23 0.106 - 0.133: 18 Chirality restraints: 468 Sorted by residual: chirality pdb=" CA ILE A 355 " pdb=" N ILE A 355 " pdb=" C ILE A 355 " pdb=" CB ILE A 355 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL A 392 " pdb=" N VAL A 392 " pdb=" C VAL A 392 " pdb=" CB VAL A 392 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA VAL H 79 " pdb=" N VAL H 79 " pdb=" C VAL H 79 " pdb=" CB VAL H 79 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 465 not shown) Planarity restraints: 579 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 45 " 0.015 5.00e-02 4.00e+02 2.33e-02 8.72e-01 pdb=" N PRO L 46 " -0.040 5.00e-02 4.00e+02 pdb=" CA PRO L 46 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO L 46 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN H 13 " 0.015 5.00e-02 4.00e+02 2.27e-02 8.22e-01 pdb=" N PRO H 14 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO H 14 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO H 14 " 0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 369 " -0.014 5.00e-02 4.00e+02 2.10e-02 7.06e-01 pdb=" N PRO A 370 " 0.036 5.00e-02 4.00e+02 pdb=" CA PRO A 370 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 370 " -0.012 5.00e-02 4.00e+02 ... (remaining 576 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 998 2.82 - 3.34: 2668 3.34 - 3.86: 5033 3.86 - 4.38: 6031 4.38 - 4.90: 10562 Nonbonded interactions: 25292 Sorted by model distance: nonbonded pdb=" OD1 ASP L 84 " pdb=" OH TYR L 88 " model vdw 2.298 2.440 nonbonded pdb=" O PHE H 29 " pdb=" NH2 ARG H 72 " model vdw 2.336 2.520 nonbonded pdb=" OD1 ASP A 361 " pdb=" OG SER A 363 " model vdw 2.342 2.440 nonbonded pdb=" OG SER A 490 " pdb=" O ARG H 112 " model vdw 2.352 2.440 nonbonded pdb=" OG SER L 69 " pdb=" OG1 THR L 72 " model vdw 2.378 2.440 ... (remaining 25287 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 4.190 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.380 Find NCS groups from input model: 0.020 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 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 : 0.002 0.018 3310 Z= 0.121 Angle : 0.488 5.508 4494 Z= 0.265 Chirality : 0.042 0.133 468 Planarity : 0.003 0.023 579 Dihedral : 9.320 59.680 1155 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.63 % Allowed : 5.56 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.45 (0.44), residues: 403 helix: -3.83 (0.67), residues: 20 sheet: 0.62 (0.43), residues: 133 loop : 0.63 (0.44), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 433 HIS 0.001 0.000 HIS H 113 PHE 0.004 0.001 PHE H 27 TYR 0.008 0.001 TYR H 95 ARG 0.001 0.000 ARG H 87 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: H 64 VAL cc_start: 0.7737 (m) cc_final: 0.7352 (m) REVERT: L 91 SER cc_start: 0.9076 (t) cc_final: 0.8731 (p) outliers start: 9 outliers final: 3 residues processed: 87 average time/residue: 0.1853 time to fit residues: 18.8761 Evaluate side-chains 62 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 59 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 9.9990 chunk 30 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 471 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3310 Z= 0.244 Angle : 0.515 5.260 4494 Z= 0.268 Chirality : 0.045 0.131 468 Planarity : 0.003 0.021 579 Dihedral : 5.378 49.011 463 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.05 % Allowed : 12.57 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.18 (0.42), residues: 403 helix: -3.87 (0.69), residues: 19 sheet: 0.40 (0.42), residues: 127 loop : 0.42 (0.42), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 433 HIS 0.002 0.001 HIS H 113 PHE 0.020 0.002 PHE H 68 TYR 0.014 0.001 TYR H 95 ARG 0.004 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 62 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 458 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8421 (tt) REVERT: L 91 SER cc_start: 0.9234 (t) cc_final: 0.8918 (p) outliers start: 7 outliers final: 5 residues processed: 68 average time/residue: 0.1718 time to fit residues: 14.0088 Evaluate side-chains 60 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 54 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 450 TYR Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.0670 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 overall best weight: 1.2924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3310 Z= 0.205 Angle : 0.511 5.776 4494 Z= 0.257 Chirality : 0.044 0.129 468 Planarity : 0.003 0.021 579 Dihedral : 5.430 50.560 463 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.34 % Allowed : 14.04 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.42), residues: 403 helix: -3.48 (0.69), residues: 27 sheet: 0.08 (0.40), residues: 141 loop : 0.46 (0.43), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 433 HIS 0.001 0.000 HIS H 113 PHE 0.026 0.001 PHE H 68 TYR 0.013 0.001 TYR H 95 ARG 0.002 0.000 ARG H 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 458 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8458 (tt) REVERT: L 91 SER cc_start: 0.9229 (t) cc_final: 0.8890 (p) outliers start: 8 outliers final: 6 residues processed: 62 average time/residue: 0.1549 time to fit residues: 11.7488 Evaluate side-chains 63 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3310 Z= 0.213 Angle : 0.511 5.804 4494 Z= 0.259 Chirality : 0.044 0.130 468 Planarity : 0.003 0.021 579 Dihedral : 5.577 57.248 463 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.22 % Allowed : 14.33 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.13 (0.42), residues: 403 helix: -3.47 (0.70), residues: 27 sheet: -0.05 (0.40), residues: 145 loop : 0.50 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 433 HIS 0.002 0.000 HIS H 113 PHE 0.024 0.001 PHE H 68 TYR 0.012 0.001 TYR H 95 ARG 0.001 0.000 ARG H 112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 60 time to evaluate : 0.360 Fit side-chains revert: symmetry clash REVERT: A 458 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8432 (tt) REVERT: L 91 SER cc_start: 0.9244 (t) cc_final: 0.8904 (p) outliers start: 11 outliers final: 7 residues processed: 67 average time/residue: 0.1517 time to fit residues: 12.5371 Evaluate side-chains 63 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 55 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 9 optimal weight: 0.0020 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3310 Z= 0.269 Angle : 0.546 5.988 4494 Z= 0.277 Chirality : 0.045 0.131 468 Planarity : 0.003 0.022 579 Dihedral : 5.667 54.203 463 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.22 % Allowed : 16.67 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.28 (0.41), residues: 403 helix: -3.53 (0.70), residues: 27 sheet: -0.19 (0.40), residues: 143 loop : 0.41 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 121 HIS 0.002 0.001 HIS H 113 PHE 0.027 0.002 PHE H 68 TYR 0.016 0.001 TYR H 114 ARG 0.002 0.000 ARG A 505 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.360 Fit side-chains REVERT: A 458 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8441 (tt) REVERT: H 82 GLN cc_start: 0.7683 (mt0) cc_final: 0.7069 (mt0) REVERT: L 91 SER cc_start: 0.9270 (t) cc_final: 0.8940 (p) outliers start: 11 outliers final: 8 residues processed: 65 average time/residue: 0.1619 time to fit residues: 12.8329 Evaluate side-chains 65 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 56 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain H residue 119 ASP Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.0970 chunk 38 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 37 optimal weight: 10.0000 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 402 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3310 Z= 0.191 Angle : 0.508 6.321 4494 Z= 0.255 Chirality : 0.044 0.129 468 Planarity : 0.003 0.022 579 Dihedral : 5.570 52.709 463 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.92 % Allowed : 17.54 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.26 (0.41), residues: 403 helix: -3.49 (0.71), residues: 27 sheet: -0.02 (0.41), residues: 128 loop : 0.28 (0.41), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 433 HIS 0.001 0.000 HIS A 442 PHE 0.023 0.001 PHE H 68 TYR 0.014 0.001 TYR H 114 ARG 0.002 0.000 ARG H 112 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 60 time to evaluate : 0.325 Fit side-chains REVERT: L 91 SER cc_start: 0.9252 (t) cc_final: 0.8927 (p) outliers start: 10 outliers final: 7 residues processed: 68 average time/residue: 0.1552 time to fit residues: 12.8492 Evaluate side-chains 63 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3310 Z= 0.170 Angle : 0.502 6.696 4494 Z= 0.251 Chirality : 0.043 0.128 468 Planarity : 0.003 0.022 579 Dihedral : 5.468 52.542 463 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.34 % Allowed : 18.71 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.23 (0.41), residues: 403 helix: -3.48 (0.71), residues: 27 sheet: 0.01 (0.41), residues: 129 loop : 0.29 (0.41), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 433 HIS 0.001 0.000 HIS A 442 PHE 0.021 0.001 PHE H 68 TYR 0.013 0.001 TYR H 114 ARG 0.001 0.000 ARG H 112 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.357 Fit side-chains REVERT: H 80 PHE cc_start: 0.7421 (m-80) cc_final: 0.7218 (m-80) REVERT: L 91 SER cc_start: 0.9243 (t) cc_final: 0.8933 (p) outliers start: 8 outliers final: 8 residues processed: 66 average time/residue: 0.1526 time to fit residues: 12.2817 Evaluate side-chains 66 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 35 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 21 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.3980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 436 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3310 Z= 0.108 Angle : 0.477 6.902 4494 Z= 0.237 Chirality : 0.043 0.126 468 Planarity : 0.003 0.022 579 Dihedral : 5.483 54.761 463 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.75 % Allowed : 20.47 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.09 (0.41), residues: 403 helix: -3.36 (0.71), residues: 27 sheet: 0.51 (0.43), residues: 120 loop : 0.35 (0.40), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 121 HIS 0.001 0.000 HIS H 115 PHE 0.012 0.001 PHE H 68 TYR 0.011 0.001 TYR H 114 ARG 0.002 0.000 ARG H 112 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: L 71 ASN cc_start: 0.6524 (m-40) cc_final: 0.5794 (t0) REVERT: L 91 SER cc_start: 0.9235 (t) cc_final: 0.8929 (p) outliers start: 6 outliers final: 5 residues processed: 71 average time/residue: 0.1559 time to fit residues: 13.1884 Evaluate side-chains 67 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 62 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3310 Z= 0.170 Angle : 0.534 11.334 4494 Z= 0.261 Chirality : 0.043 0.131 468 Planarity : 0.003 0.021 579 Dihedral : 5.432 54.440 463 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.34 % Allowed : 19.88 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.42), residues: 403 helix: -3.44 (0.70), residues: 27 sheet: 0.14 (0.41), residues: 139 loop : 0.53 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 47 HIS 0.002 0.000 HIS H 113 PHE 0.021 0.001 PHE H 68 TYR 0.011 0.001 TYR H 114 ARG 0.004 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 61 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: L 71 ASN cc_start: 0.6627 (m-40) cc_final: 0.5921 (t0) REVERT: L 91 SER cc_start: 0.9237 (t) cc_final: 0.8945 (p) outliers start: 8 outliers final: 8 residues processed: 65 average time/residue: 0.1664 time to fit residues: 13.1861 Evaluate side-chains 68 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 368 PHE Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 29 optimal weight: 0.0870 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.0050 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.5976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3310 Z= 0.137 Angle : 0.517 10.870 4494 Z= 0.255 Chirality : 0.043 0.138 468 Planarity : 0.003 0.021 579 Dihedral : 5.465 55.086 463 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.05 % Allowed : 21.05 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.42), residues: 403 helix: -3.64 (0.64), residues: 27 sheet: 0.22 (0.41), residues: 139 loop : 0.56 (0.43), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.001 0.000 HIS H 113 PHE 0.019 0.001 PHE H 68 TYR 0.011 0.001 TYR H 114 ARG 0.003 0.000 ARG H 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 806 Ramachandran restraints generated. 403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: L 71 ASN cc_start: 0.6386 (m-40) cc_final: 0.5750 (t0) REVERT: L 91 SER cc_start: 0.9213 (t) cc_final: 0.8918 (p) outliers start: 7 outliers final: 7 residues processed: 66 average time/residue: 0.1709 time to fit residues: 13.6150 Evaluate side-chains 66 residues out of total 345 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 59 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 464 ASP Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain H residue 68 PHE Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 114 TYR Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 106 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.140431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.111955 restraints weight = 5200.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.115041 restraints weight = 3593.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.117036 restraints weight = 2825.395| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3310 Z= 0.238 Angle : 0.563 10.357 4494 Z= 0.283 Chirality : 0.044 0.141 468 Planarity : 0.003 0.020 579 Dihedral : 5.503 53.244 463 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.22 % Allowed : 19.30 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.29 (0.41), residues: 403 helix: -4.19 (0.46), residues: 28 sheet: 0.03 (0.41), residues: 139 loop : 0.34 (0.42), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 121 HIS 0.003 0.001 HIS H 113 PHE 0.027 0.002 PHE H 68 TYR 0.024 0.001 TYR A 470 ARG 0.002 0.000 ARG H 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1326.19 seconds wall clock time: 25 minutes 53.78 seconds (1553.78 seconds total)