Starting phenix.real_space_refine on Sun Mar 10 15:10:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz0_26201/03_2024/7tz0_26201.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz0_26201/03_2024/7tz0_26201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz0_26201/03_2024/7tz0_26201.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz0_26201/03_2024/7tz0_26201.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz0_26201/03_2024/7tz0_26201.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tz0_26201/03_2024/7tz0_26201.pdb" } resolution = 4.17 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= 0.100 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 12 5.16 5 C 1699 2.51 5 N 453 2.21 5 O 510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2674 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1521 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 10, 'TRANS': 181} Chain: "B" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1153 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Time building chain proxies: 1.95, per 1000 atoms: 0.73 Number of scatterers: 2674 At special positions: 0 Unit cell: (58.491, 66.348, 96.903, 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 12 16.00 O 510 8.00 N 453 7.00 C 1699 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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: 1.01 Conformation dependent library (CDL) restraints added in 480.1 milliseconds 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 632 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 36.9% alpha, 5.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.304A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'B' and resid 16 through 25 removed outlier: 3.542A pdb=" N GLU B 20 " --> pdb=" O LYS B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 Processing helix chain 'B' and resid 49 through 58 removed outlier: 3.522A pdb=" N LEU B 53 " --> pdb=" O THR B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 69 removed outlier: 4.064A pdb=" N TYR B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 91 Processing helix chain 'B' and resid 93 through 103 removed outlier: 4.008A pdb=" N GLU B 97 " --> pdb=" O LEU B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 124 removed outlier: 3.528A pdb=" N ARG B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 135 removed outlier: 3.617A pdb=" N VAL B 129 " --> pdb=" O HIS B 125 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU B 130 " --> pdb=" O LEU B 126 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN B 135 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 157 removed outlier: 3.599A pdb=" N ASP B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 168 removed outlier: 3.839A pdb=" N ALA B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE B 164 " --> pdb=" O ASP B 160 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 397 through 402 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 72 hydrogen bonds defined for protein. 207 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: 0.53 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 889 1.35 - 1.46: 646 1.46 - 1.58: 1184 1.58 - 1.70: 1 1.70 - 1.81: 14 Bond restraints: 2734 Sorted by residual: bond pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 1.492 1.605 -0.113 5.00e-02 4.00e+02 5.13e+00 bond pdb=" CB PRO B 50 " pdb=" CG PRO B 50 " ideal model delta sigma weight residual 1.492 1.553 -0.061 5.00e-02 4.00e+02 1.47e+00 bond pdb=" CB LYS A 458 " pdb=" CG LYS A 458 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.11e-01 bond pdb=" CG PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 1.503 1.533 -0.030 3.40e-02 8.65e+02 8.03e-01 bond pdb=" CB ARG B 31 " pdb=" CG ARG B 31 " ideal model delta sigma weight residual 1.520 1.545 -0.025 3.00e-02 1.11e+03 6.69e-01 ... (remaining 2729 not shown) Histogram of bond angle deviations from ideal: 100.01 - 106.80: 68 106.80 - 113.60: 1439 113.60 - 120.39: 1019 120.39 - 127.18: 1166 127.18 - 133.98: 23 Bond angle restraints: 3715 Sorted by residual: angle pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 112.00 104.86 7.14 1.40e+00 5.10e-01 2.60e+01 angle pdb=" N VAL A 341 " pdb=" CA VAL A 341 " pdb=" C VAL A 341 " ideal model delta sigma weight residual 113.42 108.54 4.88 1.17e+00 7.31e-01 1.74e+01 angle pdb=" CA PRO B 50 " pdb=" N PRO B 50 " pdb=" CD PRO B 50 " ideal model delta sigma weight residual 112.00 107.42 4.58 1.40e+00 5.10e-01 1.07e+01 angle pdb=" CA LEU A 518 " pdb=" CB LEU A 518 " pdb=" CG LEU A 518 " ideal model delta sigma weight residual 116.30 125.67 -9.37 3.50e+00 8.16e-02 7.17e+00 angle pdb=" CA LYS A 458 " pdb=" CB LYS A 458 " pdb=" CG LYS A 458 " ideal model delta sigma weight residual 114.10 119.44 -5.34 2.00e+00 2.50e-01 7.14e+00 ... (remaining 3710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.80: 1429 14.80 - 29.59: 143 29.59 - 44.39: 32 44.39 - 59.18: 8 59.18 - 73.98: 2 Dihedral angle restraints: 1614 sinusoidal: 619 harmonic: 995 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 19.02 73.98 1 1.00e+01 1.00e-02 6.95e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -144.38 58.38 1 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 46.65 46.35 1 1.00e+01 1.00e-02 2.97e+01 ... (remaining 1611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 223 0.028 - 0.056: 115 0.056 - 0.084: 45 0.084 - 0.112: 19 0.112 - 0.140: 6 Chirality restraints: 408 Sorted by residual: chirality pdb=" CA PRO B 50 " pdb=" N PRO B 50 " pdb=" C PRO B 50 " pdb=" CB PRO B 50 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA PRO A 491 " pdb=" N PRO A 491 " pdb=" C PRO A 491 " pdb=" CB PRO A 491 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA VAL A 382 " pdb=" N VAL A 382 " pdb=" C VAL A 382 " pdb=" CB VAL A 382 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 405 not shown) Planarity restraints: 489 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " -0.075 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO A 384 " 0.190 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 49 " -0.056 5.00e-02 4.00e+02 8.32e-02 1.11e+01 pdb=" N PRO B 50 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 50 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 50 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 360 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C ASN A 360 " 0.036 2.00e-02 2.50e+03 pdb=" O ASN A 360 " -0.014 2.00e-02 2.50e+03 pdb=" N CYS A 361 " -0.012 2.00e-02 2.50e+03 ... (remaining 486 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 715 2.79 - 3.32: 2669 3.32 - 3.85: 4201 3.85 - 4.37: 4974 4.37 - 4.90: 7820 Nonbonded interactions: 20379 Sorted by model distance: nonbonded pdb=" OG1 THR A 415 " pdb=" OD2 ASP A 420 " model vdw 2.265 2.440 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.271 2.440 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 2.277 2.520 nonbonded pdb=" NH1 ARG A 357 " pdb=" O ILE A 358 " model vdw 2.281 2.520 nonbonded pdb=" OG1 THR B 82 " pdb=" ND1 HIS B 85 " model vdw 2.306 2.520 ... (remaining 20374 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: 0.080 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: 0.640 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.920 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6217 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 : 0.003 0.113 2734 Z= 0.226 Angle : 0.624 9.374 3715 Z= 0.330 Chirality : 0.041 0.140 408 Planarity : 0.007 0.110 489 Dihedral : 12.380 69.766 970 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.73 (0.42), residues: 343 helix: -0.69 (0.47), residues: 106 sheet: -1.48 (1.07), residues: 24 loop : -1.37 (0.40), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 79 HIS 0.004 0.001 HIS B 52 PHE 0.032 0.001 PHE A 429 TYR 0.012 0.001 TYR A 495 ARG 0.004 0.000 ARG B 31 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 418 ILE cc_start: 0.8385 (mp) cc_final: 0.7934 (mp) REVERT: A 498 GLN cc_start: 0.8587 (mp10) cc_final: 0.8268 (mp10) REVERT: B 66 LEU cc_start: 0.8491 (mt) cc_final: 0.8260 (mt) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1337 time to fit residues: 12.9903 Evaluate side-chains 72 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 20.0000 chunk 25 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 17 optimal weight: 30.0000 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6300 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 2734 Z= 0.204 Angle : 0.599 7.393 3715 Z= 0.307 Chirality : 0.043 0.134 408 Planarity : 0.005 0.054 489 Dihedral : 4.906 18.204 376 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % 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: -1.72 (0.43), residues: 343 helix: -0.59 (0.45), residues: 109 sheet: -1.27 (0.94), residues: 30 loop : -1.44 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 353 HIS 0.007 0.002 HIS B 85 PHE 0.013 0.002 PHE A 490 TYR 0.011 0.001 TYR A 380 ARG 0.003 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 374 PHE cc_start: 0.7429 (m-10) cc_final: 0.7215 (m-10) REVERT: A 409 GLN cc_start: 0.8054 (mt0) cc_final: 0.7244 (mt0) REVERT: A 418 ILE cc_start: 0.8232 (mp) cc_final: 0.7679 (mp) REVERT: A 429 PHE cc_start: 0.8121 (t80) cc_final: 0.7596 (t80) REVERT: A 442 ASP cc_start: 0.9083 (p0) cc_final: 0.8881 (p0) REVERT: A 498 GLN cc_start: 0.8453 (mp10) cc_final: 0.8117 (mp10) REVERT: B 76 MET cc_start: 0.7618 (pmm) cc_final: 0.7417 (pmm) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1174 time to fit residues: 12.3573 Evaluate side-chains 70 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 17 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 30 optimal weight: 40.0000 chunk 33 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN A 422 ASN B 36 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6328 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2734 Z= 0.199 Angle : 0.626 9.077 3715 Z= 0.312 Chirality : 0.043 0.135 408 Planarity : 0.005 0.046 489 Dihedral : 5.093 19.808 376 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.35 % Allowed : 4.58 % Favored : 95.07 % 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: -1.73 (0.43), residues: 343 helix: -0.43 (0.46), residues: 109 sheet: -2.61 (0.86), residues: 24 loop : -1.37 (0.42), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.003 0.001 HIS B 85 PHE 0.013 0.002 PHE B 150 TYR 0.013 0.001 TYR A 380 ARG 0.003 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 374 PHE cc_start: 0.7563 (m-10) cc_final: 0.7185 (m-10) REVERT: A 418 ILE cc_start: 0.8355 (mp) cc_final: 0.7858 (mp) REVERT: A 429 PHE cc_start: 0.8154 (t80) cc_final: 0.7640 (t80) REVERT: A 498 GLN cc_start: 0.8289 (mp10) cc_final: 0.7904 (mp10) outliers start: 1 outliers final: 0 residues processed: 87 average time/residue: 0.1310 time to fit residues: 13.9126 Evaluate side-chains 74 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 32 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2734 Z= 0.171 Angle : 0.612 9.450 3715 Z= 0.298 Chirality : 0.043 0.134 408 Planarity : 0.005 0.047 489 Dihedral : 4.945 19.119 376 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.04 % Favored : 90.96 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: -1.58 (0.43), residues: 343 helix: -0.38 (0.46), residues: 109 sheet: -1.69 (0.92), residues: 31 loop : -1.32 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.004 0.001 HIS B 85 PHE 0.013 0.001 PHE A 490 TYR 0.015 0.001 TYR A 380 ARG 0.003 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 418 ILE cc_start: 0.8353 (mp) cc_final: 0.7846 (mp) REVERT: A 429 PHE cc_start: 0.8156 (t80) cc_final: 0.7625 (t80) REVERT: A 498 GLN cc_start: 0.8330 (mp10) cc_final: 0.7958 (mp10) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1332 time to fit residues: 13.6640 Evaluate side-chains 72 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 40.0000 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.0270 chunk 29 optimal weight: 30.0000 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 overall best weight: 3.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2734 Z= 0.164 Angle : 0.603 9.372 3715 Z= 0.294 Chirality : 0.042 0.135 408 Planarity : 0.005 0.049 489 Dihedral : 4.869 19.188 376 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % 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: -1.53 (0.43), residues: 343 helix: -0.22 (0.47), residues: 109 sheet: -2.36 (0.91), residues: 25 loop : -1.30 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.004 0.001 HIS B 85 PHE 0.012 0.001 PHE A 490 TYR 0.015 0.001 TYR A 396 ARG 0.003 0.000 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 350 VAL cc_start: 0.8926 (p) cc_final: 0.8644 (m) REVERT: A 418 ILE cc_start: 0.8422 (mp) cc_final: 0.7860 (mp) REVERT: A 429 PHE cc_start: 0.8186 (t80) cc_final: 0.7672 (t80) REVERT: A 498 GLN cc_start: 0.8305 (mp10) cc_final: 0.7944 (mp10) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.1375 time to fit residues: 14.2335 Evaluate side-chains 74 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 8 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 27 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 20.0000 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 30.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2734 Z= 0.169 Angle : 0.620 9.492 3715 Z= 0.304 Chirality : 0.042 0.138 408 Planarity : 0.005 0.049 489 Dihedral : 4.881 18.836 376 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: -1.61 (0.43), residues: 343 helix: -0.29 (0.46), residues: 115 sheet: -1.73 (0.91), residues: 31 loop : -1.44 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 353 HIS 0.003 0.001 HIS B 85 PHE 0.012 0.001 PHE A 490 TYR 0.014 0.001 TYR A 380 ARG 0.005 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.277 Fit side-chains revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7878 (t0) cc_final: 0.7662 (t0) REVERT: A 418 ILE cc_start: 0.8451 (mp) cc_final: 0.7872 (mp) REVERT: A 429 PHE cc_start: 0.8181 (t80) cc_final: 0.7643 (t80) REVERT: A 498 GLN cc_start: 0.8288 (mp10) cc_final: 0.7934 (mp10) REVERT: B 36 ASN cc_start: 0.6199 (m110) cc_final: 0.5800 (t0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.1123 time to fit residues: 11.4105 Evaluate side-chains 68 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 50.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.4211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 2734 Z= 0.241 Angle : 0.697 12.538 3715 Z= 0.345 Chirality : 0.044 0.138 408 Planarity : 0.005 0.046 489 Dihedral : 5.460 18.850 376 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 21.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.62 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % 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: -1.94 (0.43), residues: 343 helix: -0.64 (0.43), residues: 115 sheet: -1.81 (0.94), residues: 30 loop : -1.61 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 353 HIS 0.004 0.001 HIS B 85 PHE 0.018 0.002 PHE A 490 TYR 0.014 0.002 TYR A 495 ARG 0.004 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 79 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 354 ASN cc_start: 0.8645 (m-40) cc_final: 0.8441 (m-40) REVERT: A 394 ASN cc_start: 0.7973 (t0) cc_final: 0.7745 (t0) REVERT: A 418 ILE cc_start: 0.8512 (mp) cc_final: 0.8007 (mp) REVERT: A 429 PHE cc_start: 0.8254 (t80) cc_final: 0.7709 (t80) REVERT: A 442 ASP cc_start: 0.9012 (p0) cc_final: 0.8758 (p0) REVERT: A 495 TYR cc_start: 0.7585 (m-80) cc_final: 0.7356 (m-80) REVERT: A 498 GLN cc_start: 0.8145 (mp10) cc_final: 0.7821 (mp10) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1174 time to fit residues: 11.5570 Evaluate side-chains 65 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 0.8980 chunk 25 optimal weight: 20.0000 chunk 29 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 13 optimal weight: 20.0000 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.4330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2734 Z= 0.190 Angle : 0.638 11.404 3715 Z= 0.316 Chirality : 0.043 0.143 408 Planarity : 0.005 0.046 489 Dihedral : 5.177 18.617 376 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: -1.87 (0.43), residues: 343 helix: -0.51 (0.44), residues: 115 sheet: -1.88 (0.97), residues: 29 loop : -1.60 (0.44), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 353 HIS 0.003 0.001 HIS B 85 PHE 0.023 0.002 PHE A 347 TYR 0.014 0.001 TYR A 495 ARG 0.003 0.001 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.8075 (t0) cc_final: 0.7822 (t0) REVERT: A 418 ILE cc_start: 0.8492 (mp) cc_final: 0.7949 (mp) REVERT: A 429 PHE cc_start: 0.8263 (t80) cc_final: 0.7732 (t80) REVERT: A 495 TYR cc_start: 0.7677 (m-80) cc_final: 0.7426 (m-80) REVERT: A 498 GLN cc_start: 0.8240 (mp10) cc_final: 0.7945 (mp10) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.1259 time to fit residues: 11.7777 Evaluate side-chains 68 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 0.0670 chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 overall best weight: 2.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6273 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 2734 Z= 0.156 Angle : 0.631 10.001 3715 Z= 0.307 Chirality : 0.043 0.139 408 Planarity : 0.005 0.048 489 Dihedral : 4.928 18.632 376 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.69 (0.44), residues: 343 helix: -0.30 (0.46), residues: 114 sheet: -2.44 (0.92), residues: 25 loop : -1.45 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.003 0.001 HIS B 52 PHE 0.022 0.001 PHE A 347 TYR 0.013 0.001 TYR A 495 ARG 0.008 0.001 ARG A 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 394 ASN cc_start: 0.7948 (t0) cc_final: 0.7743 (t0) REVERT: A 418 ILE cc_start: 0.8472 (mp) cc_final: 0.7929 (mp) REVERT: A 429 PHE cc_start: 0.8210 (t80) cc_final: 0.7698 (t80) REVERT: A 495 TYR cc_start: 0.7737 (m-80) cc_final: 0.7501 (m-80) REVERT: A 498 GLN cc_start: 0.8195 (mp10) cc_final: 0.7878 (mp10) outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 0.1329 time to fit residues: 13.0245 Evaluate side-chains 68 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 0.0870 chunk 8 optimal weight: 0.0070 chunk 24 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 overall best weight: 1.1380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6228 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 2734 Z= 0.142 Angle : 0.606 8.615 3715 Z= 0.293 Chirality : 0.043 0.136 408 Planarity : 0.004 0.048 489 Dihedral : 4.544 17.793 376 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.35 % Allowed : 0.35 % Favored : 99.30 % 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: -1.50 (0.44), residues: 343 helix: -0.09 (0.47), residues: 113 sheet: -2.43 (0.93), residues: 25 loop : -1.34 (0.44), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 353 HIS 0.003 0.001 HIS B 85 PHE 0.017 0.001 PHE A 347 TYR 0.013 0.001 TYR A 495 ARG 0.004 0.000 ARG A 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 686 Ramachandran restraints generated. 343 Oldfield, 0 Emsley, 343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 418 ILE cc_start: 0.8484 (mp) cc_final: 0.7919 (mp) REVERT: A 429 PHE cc_start: 0.8226 (t80) cc_final: 0.7720 (t80) REVERT: A 442 ASP cc_start: 0.8785 (p0) cc_final: 0.8436 (p0) REVERT: A 495 TYR cc_start: 0.7755 (m-80) cc_final: 0.7553 (m-80) REVERT: A 498 GLN cc_start: 0.8327 (mp10) cc_final: 0.7993 (mp10) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.1297 time to fit residues: 12.7103 Evaluate side-chains 69 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 23 optimal weight: 40.0000 chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.185578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.158891 restraints weight = 7088.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.163118 restraints weight = 4881.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.166301 restraints weight = 3596.780| |-----------------------------------------------------------------------------| r_work (final): 0.4174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6469 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2734 Z= 0.198 Angle : 0.630 10.308 3715 Z= 0.316 Chirality : 0.043 0.137 408 Planarity : 0.005 0.048 489 Dihedral : 4.934 18.381 376 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -1.81 (0.43), residues: 343 helix: -0.33 (0.45), residues: 112 sheet: -2.58 (0.87), residues: 26 loop : -1.54 (0.43), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 353 HIS 0.004 0.001 HIS B 85 PHE 0.020 0.002 PHE A 347 TYR 0.013 0.001 TYR A 495 ARG 0.006 0.001 ARG A 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 967.62 seconds wall clock time: 17 minutes 57.88 seconds (1077.88 seconds total)