Starting phenix.real_space_refine on Tue Feb 13 07:51:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc7_12141/02_2024/7bc7_12141_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc7_12141/02_2024/7bc7_12141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc7_12141/02_2024/7bc7_12141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc7_12141/02_2024/7bc7_12141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc7_12141/02_2024/7bc7_12141_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc7_12141/02_2024/7bc7_12141_updated.pdb" } resolution = 3.3 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= 0.053 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 22 5.16 5 C 2734 2.51 5 N 700 2.21 5 O 753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 59": "NH1" <-> "NH2" Residue "A GLU 85": "OE1" <-> "OE2" Residue "A ARG 183": "NH1" <-> "NH2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 300": "OE1" <-> "OE2" Residue "A GLU 338": "OE1" <-> "OE2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ARG 430": "NH1" <-> "NH2" Residue "A GLU 452": "OE1" <-> "OE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "B GLU 107": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4209 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3269 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 17, 'TRANS': 414} Chain: "B" Number of atoms: 909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 909 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 6, 'TRANS': 110} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'LYA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.86, per 1000 atoms: 0.68 Number of scatterers: 4209 At special positions: 0 Unit cell: (104.832, 64.896, 66.56, 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 22 16.00 O 753 8.00 N 700 7.00 C 2734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 72 " - pdb=" SG CYS A 306 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.04 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: 1.87 Conformation dependent library (CDL) restraints added in 809.5 milliseconds 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 992 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 16 helices and 3 sheets defined 59.7% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 30 through 59 Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 81 through 119 removed outlier: 3.921A pdb=" N THR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 111 " --> pdb=" O PHE A 107 " (cutoff:3.500A) Proline residue: A 114 - end of helix removed outlier: 3.858A pdb=" N SER A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 145 Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 150 through 161 Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 185 through 210 removed outlier: 3.920A pdb=" N GLN A 209 " --> pdb=" O VAL A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 236 removed outlier: 3.806A pdb=" N LEU A 236 " --> pdb=" O TYR A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 263 removed outlier: 4.111A pdb=" N LEU A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 299 removed outlier: 3.945A pdb=" N LEU A 275 " --> pdb=" O SER A 271 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 294 " --> pdb=" O PHE A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 335 removed outlier: 3.759A pdb=" N ALA A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N TYR A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LEU A 324 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N GLY A 328 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 358 removed outlier: 4.042A pdb=" N ALA A 343 " --> pdb=" O ASP A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 372 Processing helix chain 'A' and resid 376 through 390 removed outlier: 4.051A pdb=" N ALA A 379 " --> pdb=" O SER A 376 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N THR A 380 " --> pdb=" O MET A 377 " (cutoff:3.500A) Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 396 through 424 Proline residue: A 423 - end of helix Processing helix chain 'A' and resid 432 through 455 removed outlier: 3.821A pdb=" N LEU A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.801A pdb=" N VAL B 5 " --> pdb=" O ALA B 23 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 18 " --> pdb=" O MET B 83 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 20 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN B 82 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 34 through 36 removed outlier: 3.778A pdb=" N SER B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 92 through 94 251 hydrogen bonds defined for protein. 645 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 657 1.31 - 1.43: 1206 1.43 - 1.56: 2415 1.56 - 1.68: 0 1.68 - 1.81: 33 Bond restraints: 4311 Sorted by residual: bond pdb=" C20 LYA A 501 " pdb=" N22 LYA A 501 " ideal model delta sigma weight residual 1.340 1.468 -0.128 2.00e-02 2.50e+03 4.09e+01 bond pdb=" C17 LYA A 501 " pdb=" N19 LYA A 501 " ideal model delta sigma weight residual 1.344 1.450 -0.106 2.00e-02 2.50e+03 2.79e+01 bond pdb=" C13 LYA A 501 " pdb=" C14 LYA A 501 " ideal model delta sigma weight residual 1.444 1.367 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" N THR A 380 " pdb=" CA THR A 380 " ideal model delta sigma weight residual 1.462 1.494 -0.032 9.50e-03 1.11e+04 1.16e+01 bond pdb=" C13 LYA A 501 " pdb=" C9 LYA A 501 " ideal model delta sigma weight residual 1.434 1.366 0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 4306 not shown) Histogram of bond angle deviations from ideal: 97.36 - 106.17: 98 106.17 - 114.97: 2584 114.97 - 123.77: 3065 123.77 - 132.58: 112 132.58 - 141.38: 14 Bond angle restraints: 5873 Sorted by residual: angle pdb=" C10 LYA A 501 " pdb=" C9 LYA A 501 " pdb=" C8 LYA A 501 " ideal model delta sigma weight residual 126.87 110.82 16.05 3.00e+00 1.11e-01 2.86e+01 angle pdb=" C13 LYA A 501 " pdb=" C9 LYA A 501 " pdb=" C8 LYA A 501 " ideal model delta sigma weight residual 126.91 141.38 -14.47 3.00e+00 1.11e-01 2.33e+01 angle pdb=" N18 LYA A 501 " pdb=" C17 LYA A 501 " pdb=" N19 LYA A 501 " ideal model delta sigma weight residual 116.30 129.65 -13.35 3.00e+00 1.11e-01 1.98e+01 angle pdb=" CA VAL A 382 " pdb=" C VAL A 382 " pdb=" O VAL A 382 " ideal model delta sigma weight residual 121.27 117.50 3.77 1.04e+00 9.25e-01 1.31e+01 angle pdb=" N LEU A 387 " pdb=" CA LEU A 387 " pdb=" C LEU A 387 " ideal model delta sigma weight residual 111.28 107.84 3.44 1.09e+00 8.42e-01 9.95e+00 ... (remaining 5868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 2197 17.17 - 34.34: 255 34.34 - 51.51: 35 51.51 - 68.68: 10 68.68 - 85.85: 8 Dihedral angle restraints: 2505 sinusoidal: 940 harmonic: 1565 Sorted by residual: dihedral pdb=" CA GLU A 267 " pdb=" C GLU A 267 " pdb=" N ASP A 268 " pdb=" CA ASP A 268 " ideal model delta harmonic sigma weight residual -180.00 -156.42 -23.58 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CB CYS A 72 " pdb=" SG CYS A 72 " pdb=" SG CYS A 306 " pdb=" CB CYS A 306 " ideal model delta sinusoidal sigma weight residual 93.00 130.28 -37.28 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CA TYR B 80 " pdb=" C TYR B 80 " pdb=" N LEU B 81 " pdb=" CA LEU B 81 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 ... (remaining 2502 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 398 0.041 - 0.082: 194 0.082 - 0.124: 64 0.124 - 0.165: 13 0.165 - 0.206: 3 Chirality restraints: 672 Sorted by residual: chirality pdb=" C23 LYA A 501 " pdb=" C24 LYA A 501 " pdb=" C29 LYA A 501 " pdb=" N22 LYA A 501 " both_signs ideal model delta sigma weight residual False -2.46 -2.67 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR A 363 " pdb=" N THR A 363 " pdb=" C THR A 363 " pdb=" CB THR A 363 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.20 2.00e-01 2.50e+01 9.78e-01 chirality pdb=" CA LEU A 387 " pdb=" N LEU A 387 " pdb=" C LEU A 387 " pdb=" CB LEU A 387 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.79e-01 ... (remaining 669 not shown) Planarity restraints: 733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 216 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C TYR A 216 " -0.031 2.00e-02 2.50e+03 pdb=" O TYR A 216 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 217 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 432 " -0.026 5.00e-02 4.00e+02 3.94e-02 2.49e+00 pdb=" N PRO A 433 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 433 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 433 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 443 " -0.025 5.00e-02 4.00e+02 3.81e-02 2.33e+00 pdb=" N PRO A 444 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 444 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 444 " -0.022 5.00e-02 4.00e+02 ... (remaining 730 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 81 2.67 - 3.23: 4264 3.23 - 3.78: 6614 3.78 - 4.34: 8876 4.34 - 4.90: 14986 Nonbonded interactions: 34821 Sorted by model distance: nonbonded pdb=" O LYS A 249 " pdb=" OG1 THR A 252 " model vdw 2.110 2.440 nonbonded pdb=" O TYR A 299 " pdb=" NH2 ARG A 430 " model vdw 2.233 2.520 nonbonded pdb=" NH1 ARG A 156 " pdb=" OD2 ASP A 164 " model vdw 2.268 2.520 nonbonded pdb=" O SER A 28 " pdb=" OH TYR A 233 " model vdw 2.274 2.440 nonbonded pdb=" O GLY A 113 " pdb=" OG SER A 116 " model vdw 2.282 2.440 ... (remaining 34816 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 6.900 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.740 Find NCS groups from input model: 0.120 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.009 0.128 4311 Z= 0.583 Angle : 0.978 16.055 5873 Z= 0.493 Chirality : 0.053 0.206 672 Planarity : 0.005 0.039 733 Dihedral : 15.119 85.854 1507 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.36 % Favored : 90.46 % Rotamer: Outliers : 0.23 % Allowed : 1.37 % Favored : 98.40 % 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: -1.48 (0.36), residues: 545 helix: 0.54 (0.29), residues: 325 sheet: -3.74 (0.63), residues: 54 loop : -3.06 (0.44), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 36 HIS 0.005 0.002 HIS A 427 PHE 0.016 0.002 PHE A 103 TYR 0.024 0.002 TYR A 299 ARG 0.010 0.001 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 103 time to evaluate : 0.496 Fit side-chains REVERT: A 332 LEU cc_start: 0.8018 (tp) cc_final: 0.7815 (tp) REVERT: A 377 MET cc_start: 0.7508 (mtm) cc_final: 0.7274 (mtm) REVERT: B 57 ASP cc_start: 0.8199 (t70) cc_final: 0.7880 (t70) outliers start: 1 outliers final: 0 residues processed: 104 average time/residue: 0.1322 time to fit residues: 18.0822 Evaluate side-chains 90 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4311 Z= 0.230 Angle : 0.665 8.513 5873 Z= 0.325 Chirality : 0.042 0.153 672 Planarity : 0.005 0.042 733 Dihedral : 8.667 87.817 612 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.92 % Allowed : 9.84 % Favored : 89.24 % 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: -0.91 (0.37), residues: 545 helix: 0.80 (0.29), residues: 335 sheet: -3.59 (0.73), residues: 40 loop : -2.70 (0.45), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 450 HIS 0.002 0.001 HIS B 50 PHE 0.013 0.001 PHE A 436 TYR 0.015 0.001 TYR A 422 ARG 0.004 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 101 time to evaluate : 0.472 Fit side-chains REVERT: A 332 LEU cc_start: 0.7876 (tp) cc_final: 0.7647 (tp) REVERT: A 377 MET cc_start: 0.7536 (mtm) cc_final: 0.7301 (mtm) REVERT: B 57 ASP cc_start: 0.8188 (t70) cc_final: 0.7909 (t70) outliers start: 4 outliers final: 3 residues processed: 102 average time/residue: 0.1321 time to fit residues: 17.8124 Evaluate side-chains 90 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain B residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4311 Z= 0.245 Angle : 0.638 8.932 5873 Z= 0.311 Chirality : 0.041 0.154 672 Planarity : 0.005 0.042 733 Dihedral : 8.117 88.506 612 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.52 % Allowed : 15.79 % Favored : 81.69 % 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: -0.78 (0.37), residues: 545 helix: 0.89 (0.29), residues: 334 sheet: -3.41 (0.70), residues: 39 loop : -2.65 (0.44), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 450 HIS 0.004 0.001 HIS B 50 PHE 0.011 0.002 PHE A 283 TYR 0.015 0.001 TYR A 299 ARG 0.004 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 89 time to evaluate : 0.510 Fit side-chains REVERT: A 332 LEU cc_start: 0.7896 (tp) cc_final: 0.7648 (tp) REVERT: A 366 MET cc_start: 0.8304 (tpp) cc_final: 0.7888 (tpp) REVERT: A 377 MET cc_start: 0.7629 (mtm) cc_final: 0.7386 (mtm) REVERT: B 57 ASP cc_start: 0.8219 (t70) cc_final: 0.7962 (t70) outliers start: 11 outliers final: 9 residues processed: 97 average time/residue: 0.1311 time to fit residues: 17.0030 Evaluate side-chains 94 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 27 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4311 Z= 0.210 Angle : 0.611 8.812 5873 Z= 0.296 Chirality : 0.040 0.149 672 Planarity : 0.005 0.042 733 Dihedral : 7.812 86.190 612 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.75 % Allowed : 18.99 % Favored : 78.26 % 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: -0.55 (0.37), residues: 545 helix: 1.04 (0.29), residues: 333 sheet: -3.25 (0.70), residues: 39 loop : -2.45 (0.44), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 450 HIS 0.004 0.001 HIS B 50 PHE 0.012 0.001 PHE A 283 TYR 0.015 0.001 TYR A 299 ARG 0.005 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 0.472 Fit side-chains REVERT: A 40 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.7886 (tp) REVERT: A 332 LEU cc_start: 0.7876 (tp) cc_final: 0.7627 (tp) REVERT: A 366 MET cc_start: 0.8321 (tpp) cc_final: 0.7905 (tpp) REVERT: A 377 MET cc_start: 0.7661 (mtm) cc_final: 0.7425 (mtm) REVERT: B 57 ASP cc_start: 0.8209 (t70) cc_final: 0.7995 (t70) outliers start: 12 outliers final: 6 residues processed: 103 average time/residue: 0.1520 time to fit residues: 20.0281 Evaluate side-chains 96 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain B residue 7 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 0.4980 chunk 36 optimal weight: 0.0060 chunk 26 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4311 Z= 0.183 Angle : 0.605 8.912 5873 Z= 0.288 Chirality : 0.040 0.150 672 Planarity : 0.005 0.044 733 Dihedral : 7.588 84.875 612 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.52 % Allowed : 20.37 % Favored : 77.12 % 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: -0.31 (0.37), residues: 545 helix: 1.19 (0.29), residues: 333 sheet: -3.05 (0.71), residues: 39 loop : -2.31 (0.44), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 307 HIS 0.003 0.001 HIS B 50 PHE 0.012 0.001 PHE A 283 TYR 0.010 0.001 TYR A 50 ARG 0.004 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.426 Fit side-chains REVERT: A 40 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.7928 (tp) REVERT: A 332 LEU cc_start: 0.7864 (tp) cc_final: 0.7609 (tp) REVERT: A 366 MET cc_start: 0.8291 (tpp) cc_final: 0.7883 (tpp) REVERT: A 377 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7440 (mtm) REVERT: B 57 ASP cc_start: 0.8189 (t70) cc_final: 0.7897 (t0) outliers start: 11 outliers final: 9 residues processed: 106 average time/residue: 0.1482 time to fit residues: 20.3731 Evaluate side-chains 101 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain B residue 7 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4311 Z= 0.235 Angle : 0.624 8.942 5873 Z= 0.300 Chirality : 0.041 0.154 672 Planarity : 0.005 0.044 733 Dihedral : 7.571 85.722 612 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.66 % Allowed : 20.37 % Favored : 75.97 % 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: -0.31 (0.37), residues: 545 helix: 1.17 (0.29), residues: 333 sheet: -2.61 (0.66), residues: 49 loop : -2.32 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 36 HIS 0.003 0.001 HIS B 50 PHE 0.012 0.002 PHE A 283 TYR 0.014 0.001 TYR A 299 ARG 0.004 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.428 Fit side-chains REVERT: A 40 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.7789 (tp) REVERT: A 332 LEU cc_start: 0.7914 (tp) cc_final: 0.7649 (tp) REVERT: A 366 MET cc_start: 0.8299 (tpp) cc_final: 0.7932 (tpp) REVERT: A 377 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7413 (mtm) outliers start: 16 outliers final: 13 residues processed: 102 average time/residue: 0.1458 time to fit residues: 19.0273 Evaluate side-chains 105 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 27 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4311 Z= 0.216 Angle : 0.618 9.211 5873 Z= 0.298 Chirality : 0.041 0.147 672 Planarity : 0.005 0.043 733 Dihedral : 7.473 85.599 612 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.66 % Allowed : 20.59 % Favored : 75.74 % 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: -0.19 (0.37), residues: 545 helix: 1.24 (0.29), residues: 331 sheet: -2.56 (0.65), residues: 49 loop : -2.17 (0.46), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 307 HIS 0.003 0.001 HIS B 50 PHE 0.013 0.001 PHE A 283 TYR 0.013 0.001 TYR A 299 ARG 0.004 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.470 Fit side-chains REVERT: A 40 LEU cc_start: 0.8479 (OUTLIER) cc_final: 0.7637 (tp) REVERT: A 217 ILE cc_start: 0.8080 (OUTLIER) cc_final: 0.7858 (mp) REVERT: A 332 LEU cc_start: 0.7907 (tp) cc_final: 0.7644 (tp) REVERT: A 366 MET cc_start: 0.8268 (tpp) cc_final: 0.7896 (tpp) REVERT: A 377 MET cc_start: 0.7638 (OUTLIER) cc_final: 0.7406 (mtm) outliers start: 16 outliers final: 12 residues processed: 106 average time/residue: 0.1468 time to fit residues: 20.0683 Evaluate side-chains 110 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 95 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 27 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4311 Z= 0.224 Angle : 0.619 8.942 5873 Z= 0.300 Chirality : 0.041 0.149 672 Planarity : 0.005 0.043 733 Dihedral : 7.423 86.059 612 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.66 % Allowed : 20.37 % Favored : 75.97 % 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 (0.37), residues: 545 helix: 1.20 (0.29), residues: 333 sheet: -2.43 (0.66), residues: 49 loop : -2.28 (0.45), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 450 HIS 0.004 0.001 HIS B 50 PHE 0.013 0.001 PHE A 283 TYR 0.015 0.001 TYR A 299 ARG 0.005 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.482 Fit side-chains REVERT: A 40 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.7628 (tp) REVERT: A 217 ILE cc_start: 0.8086 (OUTLIER) cc_final: 0.7865 (mp) REVERT: A 332 LEU cc_start: 0.7921 (tp) cc_final: 0.7656 (tp) REVERT: A 366 MET cc_start: 0.8300 (tpp) cc_final: 0.7936 (tpp) REVERT: A 377 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7409 (mtm) outliers start: 16 outliers final: 13 residues processed: 107 average time/residue: 0.1447 time to fit residues: 19.9733 Evaluate side-chains 110 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 287 THR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 27 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 51 optimal weight: 0.1980 chunk 24 optimal weight: 0.0370 chunk 35 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4311 Z= 0.170 Angle : 0.587 9.472 5873 Z= 0.284 Chirality : 0.039 0.148 672 Planarity : 0.004 0.045 733 Dihedral : 7.118 85.754 612 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.97 % Allowed : 21.51 % Favored : 75.51 % 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: 0.01 (0.37), residues: 545 helix: 1.39 (0.29), residues: 331 sheet: -2.64 (0.70), residues: 39 loop : -2.08 (0.44), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 450 HIS 0.003 0.001 HIS B 50 PHE 0.013 0.001 PHE A 283 TYR 0.015 0.001 TYR A 299 ARG 0.004 0.000 ARG A 430 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 95 time to evaluate : 0.418 Fit side-chains REVERT: A 40 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.7513 (tp) REVERT: A 332 LEU cc_start: 0.7869 (tp) cc_final: 0.7610 (tp) REVERT: A 366 MET cc_start: 0.8266 (tpp) cc_final: 0.7916 (tpp) REVERT: A 377 MET cc_start: 0.7589 (OUTLIER) cc_final: 0.7376 (mtm) outliers start: 13 outliers final: 10 residues processed: 103 average time/residue: 0.1593 time to fit residues: 20.6697 Evaluate side-chains 105 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 27 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4311 Z= 0.217 Angle : 0.607 9.460 5873 Z= 0.295 Chirality : 0.040 0.156 672 Planarity : 0.004 0.043 733 Dihedral : 7.148 87.408 612 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.66 % Allowed : 21.74 % Favored : 74.60 % 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: 0.05 (0.37), residues: 545 helix: 1.38 (0.29), residues: 331 sheet: -2.07 (0.70), residues: 49 loop : -2.09 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 450 HIS 0.003 0.001 HIS B 50 PHE 0.013 0.001 PHE A 283 TYR 0.016 0.001 TYR A 299 ARG 0.004 0.000 ARG A 430 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.433 Fit side-chains REVERT: A 217 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7837 (mp) REVERT: A 332 LEU cc_start: 0.7916 (tp) cc_final: 0.7648 (tp) REVERT: A 366 MET cc_start: 0.8272 (tpp) cc_final: 0.7920 (tpp) REVERT: A 377 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7369 (mtm) REVERT: B 54 SER cc_start: 0.8776 (t) cc_final: 0.8425 (p) outliers start: 16 outliers final: 12 residues processed: 107 average time/residue: 0.1543 time to fit residues: 20.9580 Evaluate side-chains 106 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 303 SER Chi-restraints excluded: chain A residue 330 LEU Chi-restraints excluded: chain A residue 377 MET Chi-restraints excluded: chain A residue 427 HIS Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 27 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.0470 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 50 HIS ** 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 = 0.3537 r_free = 0.3537 target = 0.131209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.122656 restraints weight = 5750.382| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.71 r_work: 0.3341 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4311 Z= 0.173 Angle : 0.594 9.630 5873 Z= 0.287 Chirality : 0.040 0.157 672 Planarity : 0.004 0.045 733 Dihedral : 6.971 87.290 612 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.97 % Allowed : 22.65 % Favored : 74.37 % 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: 0.15 (0.37), residues: 545 helix: 1.43 (0.29), residues: 332 sheet: -2.53 (0.70), residues: 39 loop : -1.90 (0.44), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 450 HIS 0.004 0.001 HIS B 50 PHE 0.013 0.001 PHE A 283 TYR 0.017 0.001 TYR A 299 ARG 0.005 0.000 ARG A 430 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1387.08 seconds wall clock time: 25 minutes 39.24 seconds (1539.24 seconds total)