Starting phenix.real_space_refine on Sat Apr 6 05:49:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk1_21223/04_2024/6vk1_21223.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk1_21223/04_2024/6vk1_21223.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk1_21223/04_2024/6vk1_21223.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk1_21223/04_2024/6vk1_21223.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk1_21223/04_2024/6vk1_21223.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vk1_21223/04_2024/6vk1_21223.pdb" } resolution = 3.9 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= 0.008 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 34 5.16 5 C 4712 2.51 5 N 1203 2.21 5 O 1310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 192": "OE1" <-> "OE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A ARG 180": "NH1" <-> "NH2" Residue "A GLU 316": "OE1" <-> "OE2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A GLU 474": "OE1" <-> "OE2" Residue "A ARG 525": "NH1" <-> "NH2" Residue "A GLU 537": "OE1" <-> "OE2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 646": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7259 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2343 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 4916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4916 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 20, 'TRANS': 581} Chain breaks: 5 Time building chain proxies: 4.25, per 1000 atoms: 0.59 Number of scatterers: 7259 At special positions: 0 Unit cell: (78.3, 99.9, 152.55, 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 34 16.00 O 1310 8.00 N 1203 7.00 C 4712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.77 Conformation dependent library (CDL) restraints added in 1.2 seconds 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1700 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 0 sheets defined 79.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'B' and resid 3 through 31 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 44 through 71 Processing helix chain 'B' and resid 75 through 98 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 99 through 100 No H-bonds generated for 'chain 'B' and resid 99 through 100' Processing helix chain 'B' and resid 101 through 104 Processing helix chain 'B' and resid 105 through 135 removed outlier: 3.856A pdb=" N ALA B 109 " --> pdb=" O PHE B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 175 Processing helix chain 'B' and resid 179 through 220 removed outlier: 3.560A pdb=" N THR B 183 " --> pdb=" O ASP B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 294 removed outlier: 4.022A pdb=" N TYR B 270 " --> pdb=" O GLY B 266 " (cutoff:3.500A) Proline residue: B 292 - end of helix Processing helix chain 'B' and resid 297 through 324 Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 42 through 47 Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 83 through 100 removed outlier: 3.583A pdb=" N PHE A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.877A pdb=" N THR A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 138 Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.676A pdb=" N ILE A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 184 removed outlier: 3.604A pdb=" N ALA A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.601A pdb=" N LYS A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY A 200 " --> pdb=" O LYS A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 224 removed outlier: 4.131A pdb=" N SER A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.630A pdb=" N TRP A 230 " --> pdb=" O SER A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 329 removed outlier: 4.318A pdb=" N ILE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE A 320 " --> pdb=" O GLU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 removed outlier: 3.932A pdb=" N ALA A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 361 removed outlier: 5.558A pdb=" N ASP A 359 " --> pdb=" O PRO A 356 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN A 360 " --> pdb=" O HIS A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 383 removed outlier: 4.058A pdb=" N TYR A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 407 removed outlier: 3.931A pdb=" N ARG A 407 " --> pdb=" O GLU A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 426 removed outlier: 3.869A pdb=" N TYR A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 removed outlier: 3.995A pdb=" N ALA A 433 " --> pdb=" O ASN A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 461 Processing helix chain 'A' and resid 462 through 465 removed outlier: 4.080A pdb=" N LYS A 465 " --> pdb=" O PRO A 462 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 465' Processing helix chain 'A' and resid 468 through 480 Processing helix chain 'A' and resid 481 through 495 removed outlier: 3.708A pdb=" N TYR A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 517 removed outlier: 3.767A pdb=" N THR A 505 " --> pdb=" O SER A 501 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 removed outlier: 3.911A pdb=" N THR A 526 " --> pdb=" O PRO A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 548 removed outlier: 4.023A pdb=" N ALA A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU A 548 " --> pdb=" O SER A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.805A pdb=" N SER A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 609 removed outlier: 3.683A pdb=" N VAL A 600 " --> pdb=" O ILE A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 624 removed outlier: 3.662A pdb=" N LEU A 618 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 647 through 662 removed outlier: 3.686A pdb=" N ASP A 662 " --> pdb=" O VAL A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 682 498 hydrogen bonds defined for protein. 1488 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: 1.88 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2267 1.34 - 1.46: 1464 1.46 - 1.58: 3645 1.58 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 7437 Sorted by residual: bond pdb=" N HIS B 101 " pdb=" CA HIS B 101 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.29e-02 6.01e+03 7.91e+00 bond pdb=" N GLU B 102 " pdb=" CA GLU B 102 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.27e-02 6.20e+03 6.07e+00 bond pdb=" N ARG B 103 " pdb=" CA ARG B 103 " ideal model delta sigma weight residual 1.459 1.486 -0.028 1.16e-02 7.43e+03 5.72e+00 bond pdb=" CE1 HIS B 101 " pdb=" NE2 HIS B 101 " ideal model delta sigma weight residual 1.321 1.338 -0.017 1.00e-02 1.00e+04 3.03e+00 bond pdb=" CA HIS B 101 " pdb=" C HIS B 101 " ideal model delta sigma weight residual 1.523 1.538 -0.015 1.34e-02 5.57e+03 1.30e+00 ... (remaining 7432 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.48: 164 106.48 - 113.38: 3953 113.38 - 120.28: 2882 120.28 - 127.19: 2995 127.19 - 134.09: 71 Bond angle restraints: 10065 Sorted by residual: angle pdb=" N GLY A 253 " pdb=" CA GLY A 253 " pdb=" C GLY A 253 " ideal model delta sigma weight residual 112.48 118.47 -5.99 1.21e+00 6.83e-01 2.45e+01 angle pdb=" C ASN A 533 " pdb=" N ASP A 534 " pdb=" CA ASP A 534 " ideal model delta sigma weight residual 121.54 127.96 -6.42 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C PHE A 201 " pdb=" N ASN A 202 " pdb=" CA ASN A 202 " ideal model delta sigma weight residual 121.54 127.39 -5.85 1.91e+00 2.74e-01 9.38e+00 angle pdb=" CA ARG B 103 " pdb=" C ARG B 103 " pdb=" O ARG B 103 " ideal model delta sigma weight residual 121.07 117.91 3.16 1.10e+00 8.26e-01 8.26e+00 angle pdb=" C PHE B 214 " pdb=" N TYR B 215 " pdb=" CA TYR B 215 " ideal model delta sigma weight residual 120.79 124.54 -3.75 1.39e+00 5.18e-01 7.29e+00 ... (remaining 10060 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 3880 17.65 - 35.31: 440 35.31 - 52.96: 64 52.96 - 70.61: 14 70.61 - 88.26: 5 Dihedral angle restraints: 4403 sinusoidal: 1772 harmonic: 2631 Sorted by residual: dihedral pdb=" CA ASN A 645 " pdb=" C ASN A 645 " pdb=" N ARG A 646 " pdb=" CA ARG A 646 " ideal model delta harmonic sigma weight residual 180.00 157.61 22.39 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA ALA A 38 " pdb=" C ALA A 38 " pdb=" N LYS A 39 " pdb=" CA LYS A 39 " ideal model delta harmonic sigma weight residual -180.00 -160.05 -19.95 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA SER A 245 " pdb=" C SER A 245 " pdb=" N ASP A 246 " pdb=" CA ASP A 246 " ideal model delta harmonic sigma weight residual 180.00 160.30 19.70 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 4400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 784 0.037 - 0.075: 265 0.075 - 0.112: 46 0.112 - 0.149: 10 0.149 - 0.187: 1 Chirality restraints: 1106 Sorted by residual: chirality pdb=" CA LEU A 252 " pdb=" N LEU A 252 " pdb=" C LEU A 252 " pdb=" CB LEU A 252 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CB VAL B 155 " pdb=" CA VAL B 155 " pdb=" CG1 VAL B 155 " pdb=" CG2 VAL B 155 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA VAL A 203 " pdb=" N VAL A 203 " pdb=" C VAL A 203 " pdb=" CB VAL A 203 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.28e-01 ... (remaining 1103 not shown) Planarity restraints: 1257 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 295 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.01e+00 pdb=" N PRO B 296 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 2 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO B 3 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 3 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 3 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 102 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.41e+00 pdb=" C GLU B 102 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU B 102 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG B 103 " -0.009 2.00e-02 2.50e+03 ... (remaining 1254 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1500 2.78 - 3.31: 7437 3.31 - 3.84: 11683 3.84 - 4.37: 12815 4.37 - 4.90: 21844 Nonbonded interactions: 55279 Sorted by model distance: nonbonded pdb=" O THR B 144 " pdb=" OG SER B 148 " model vdw 2.245 2.440 nonbonded pdb=" CD1 LEU B 285 " pdb=" ND1 HIS B 286 " model vdw 2.250 3.540 nonbonded pdb=" O ASP B 179 " pdb=" OG SER B 182 " model vdw 2.280 2.440 nonbonded pdb=" OH TYR A 425 " pdb=" OE1 GLN A 453 " model vdw 2.293 2.440 nonbonded pdb=" OH TYR B 104 " pdb=" OD2 ASP B 179 " model vdw 2.296 2.440 ... (remaining 55274 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: 0.170 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: 0.000 Extract box with map and model: 1.280 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 22.650 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 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 0.036 7437 Z= 0.174 Angle : 0.590 6.422 10065 Z= 0.362 Chirality : 0.038 0.187 1106 Planarity : 0.004 0.043 1257 Dihedral : 14.769 88.262 2703 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.13 % Allowed : 5.08 % Favored : 94.80 % 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: -1.86 (0.25), residues: 866 helix: -0.46 (0.18), residues: 659 sheet: None (None), residues: 0 loop : -3.52 (0.32), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 27 HIS 0.004 0.001 HIS A 143 PHE 0.013 0.001 PHE B 147 TYR 0.011 0.001 TYR A 74 ARG 0.003 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 237 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8411 (mt0) cc_final: 0.8099 (tm-30) REVERT: B 60 THR cc_start: 0.9237 (p) cc_final: 0.8945 (p) REVERT: B 85 ARG cc_start: 0.8645 (mmt180) cc_final: 0.7809 (mmm160) REVERT: B 103 ARG cc_start: 0.5868 (mpp80) cc_final: 0.4330 (ptm-80) REVERT: B 118 LEU cc_start: 0.8831 (mt) cc_final: 0.8259 (mt) REVERT: B 119 LYS cc_start: 0.9163 (mtmt) cc_final: 0.8932 (mtpp) REVERT: B 122 HIS cc_start: 0.8242 (m90) cc_final: 0.7997 (m170) REVERT: B 124 ILE cc_start: 0.9062 (pt) cc_final: 0.8740 (pt) REVERT: B 197 LEU cc_start: 0.9220 (tp) cc_final: 0.8927 (tp) REVERT: B 202 ASN cc_start: 0.7890 (t0) cc_final: 0.7326 (t0) REVERT: B 206 GLN cc_start: 0.7832 (mt0) cc_final: 0.7278 (mt0) REVERT: A 149 LEU cc_start: 0.9375 (tp) cc_final: 0.9067 (mm) REVERT: A 238 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7682 (mt-10) REVERT: A 416 CYS cc_start: 0.8270 (m) cc_final: 0.8053 (m) REVERT: A 639 GLU cc_start: 0.8036 (pp20) cc_final: 0.7656 (pt0) REVERT: A 642 LEU cc_start: 0.6236 (pp) cc_final: 0.5211 (pp) REVERT: A 676 LEU cc_start: 0.7656 (tp) cc_final: 0.7311 (tp) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.2140 time to fit residues: 65.7474 Evaluate side-chains 169 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 HIS B 189 GLN A 86 GLN A 101 ASN A 113 HIS A 202 ASN ** A 504 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 578 GLN A 593 GLN A 620 GLN ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7437 Z= 0.272 Angle : 0.636 13.445 10065 Z= 0.331 Chirality : 0.041 0.200 1106 Planarity : 0.004 0.047 1257 Dihedral : 4.610 22.783 973 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.05 % Allowed : 15.74 % Favored : 81.22 % 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 (0.27), residues: 866 helix: 0.94 (0.19), residues: 662 sheet: None (None), residues: 0 loop : -3.14 (0.34), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 27 HIS 0.007 0.001 HIS B 122 PHE 0.021 0.002 PHE B 293 TYR 0.016 0.002 TYR A 486 ARG 0.003 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8551 (mt0) cc_final: 0.8233 (tm-30) REVERT: B 60 THR cc_start: 0.9256 (p) cc_final: 0.9014 (p) REVERT: B 83 PHE cc_start: 0.6691 (t80) cc_final: 0.6439 (t80) REVERT: B 85 ARG cc_start: 0.8883 (mmt180) cc_final: 0.7713 (mmm160) REVERT: B 103 ARG cc_start: 0.5904 (mpp80) cc_final: 0.3896 (ttp-170) REVERT: B 128 ARG cc_start: 0.7976 (mmm160) cc_final: 0.7767 (mmm160) REVERT: B 187 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7637 (tt) REVERT: B 197 LEU cc_start: 0.9292 (tp) cc_final: 0.8863 (tp) REVERT: B 298 MET cc_start: 0.8254 (mtt) cc_final: 0.7627 (mpp) REVERT: A 74 TYR cc_start: 0.7390 (t80) cc_final: 0.7107 (t80) REVERT: A 78 TRP cc_start: 0.8982 (t-100) cc_final: 0.8731 (t-100) REVERT: A 149 LEU cc_start: 0.9354 (tp) cc_final: 0.9076 (mm) REVERT: A 416 CYS cc_start: 0.8472 (m) cc_final: 0.8101 (m) REVERT: A 423 ASN cc_start: 0.8447 (p0) cc_final: 0.8227 (p0) REVERT: A 656 ASP cc_start: 0.7422 (m-30) cc_final: 0.7186 (m-30) outliers start: 24 outliers final: 11 residues processed: 185 average time/residue: 0.1854 time to fit residues: 46.1388 Evaluate side-chains 173 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 161 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 658 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 79 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 ASN A 638 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7437 Z= 0.182 Angle : 0.574 12.036 10065 Z= 0.296 Chirality : 0.038 0.125 1106 Planarity : 0.004 0.047 1257 Dihedral : 4.337 20.474 973 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.05 % Allowed : 18.65 % Favored : 78.30 % 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: 0.96 (0.28), residues: 866 helix: 1.62 (0.20), residues: 661 sheet: None (None), residues: 0 loop : -2.74 (0.39), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 632 HIS 0.006 0.001 HIS B 79 PHE 0.027 0.001 PHE B 293 TYR 0.012 0.001 TYR A 486 ARG 0.002 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 177 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8439 (mt0) cc_final: 0.8110 (tm-30) REVERT: B 60 THR cc_start: 0.9115 (p) cc_final: 0.8895 (p) REVERT: B 79 HIS cc_start: 0.7590 (t-90) cc_final: 0.7386 (t-90) REVERT: B 83 PHE cc_start: 0.6595 (t80) cc_final: 0.6347 (t80) REVERT: B 85 ARG cc_start: 0.8747 (mmt180) cc_final: 0.7746 (mmm160) REVERT: B 103 ARG cc_start: 0.5976 (mpp80) cc_final: 0.3679 (ttp-170) REVERT: B 128 ARG cc_start: 0.7784 (mmm160) cc_final: 0.7513 (mmm160) REVERT: B 189 GLN cc_start: 0.8818 (mp10) cc_final: 0.8559 (mp10) REVERT: B 195 MET cc_start: 0.7833 (mtp) cc_final: 0.7307 (mtp) REVERT: B 197 LEU cc_start: 0.9281 (tp) cc_final: 0.8894 (tp) REVERT: B 271 GLU cc_start: 0.7986 (pt0) cc_final: 0.7185 (pt0) REVERT: B 272 LYS cc_start: 0.8407 (mptt) cc_final: 0.7997 (mmtm) REVERT: B 298 MET cc_start: 0.8105 (mtt) cc_final: 0.7839 (mtm) REVERT: A 74 TYR cc_start: 0.7507 (t80) cc_final: 0.7144 (t80) REVERT: A 374 GLN cc_start: 0.8484 (mt0) cc_final: 0.8264 (mm110) REVERT: A 416 CYS cc_start: 0.8457 (m) cc_final: 0.8096 (m) REVERT: A 423 ASN cc_start: 0.8376 (p0) cc_final: 0.8120 (p0) outliers start: 24 outliers final: 12 residues processed: 188 average time/residue: 0.1820 time to fit residues: 46.1815 Evaluate side-chains 168 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 156 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 147 PHE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 682 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7437 Z= 0.262 Angle : 0.627 10.706 10065 Z= 0.323 Chirality : 0.040 0.218 1106 Planarity : 0.004 0.045 1257 Dihedral : 4.390 22.482 973 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.81 % Allowed : 19.92 % Favored : 76.27 % 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: 0.93 (0.28), residues: 866 helix: 1.62 (0.19), residues: 660 sheet: None (None), residues: 0 loop : -2.84 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 541 HIS 0.004 0.001 HIS B 79 PHE 0.031 0.002 PHE B 277 TYR 0.012 0.002 TYR A 636 ARG 0.002 0.000 ARG A 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8552 (mt0) cc_final: 0.8185 (tm-30) REVERT: B 60 THR cc_start: 0.9123 (p) cc_final: 0.8901 (p) REVERT: B 79 HIS cc_start: 0.7641 (t-90) cc_final: 0.7435 (t-90) REVERT: B 83 PHE cc_start: 0.6767 (t80) cc_final: 0.6496 (t80) REVERT: B 85 ARG cc_start: 0.8802 (mmt180) cc_final: 0.7862 (mmm160) REVERT: B 128 ARG cc_start: 0.7786 (mmm160) cc_final: 0.7494 (mmm160) REVERT: B 142 MET cc_start: 0.5294 (tpt) cc_final: 0.4853 (tpt) REVERT: B 195 MET cc_start: 0.8067 (mtp) cc_final: 0.7689 (mtp) REVERT: B 197 LEU cc_start: 0.9315 (tp) cc_final: 0.8885 (tp) REVERT: B 318 TRP cc_start: 0.6460 (t-100) cc_final: 0.5397 (t-100) REVERT: A 74 TYR cc_start: 0.7714 (t80) cc_final: 0.7199 (t80) REVERT: A 248 GLU cc_start: 0.7594 (mp0) cc_final: 0.7229 (mp0) REVERT: A 416 CYS cc_start: 0.8470 (m) cc_final: 0.8115 (m) REVERT: A 423 ASN cc_start: 0.8379 (p0) cc_final: 0.8089 (p0) REVERT: A 438 MET cc_start: 0.7969 (mmm) cc_final: 0.7538 (mmm) REVERT: A 620 GLN cc_start: 0.7369 (OUTLIER) cc_final: 0.7155 (tm-30) outliers start: 30 outliers final: 15 residues processed: 174 average time/residue: 0.1714 time to fit residues: 41.3539 Evaluate side-chains 168 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 278 THR Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 658 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 0.0770 chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 76 optimal weight: 0.3980 chunk 21 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7437 Z= 0.150 Angle : 0.579 10.443 10065 Z= 0.292 Chirality : 0.038 0.268 1106 Planarity : 0.004 0.055 1257 Dihedral : 4.158 26.866 973 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.17 % Allowed : 20.05 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.29), residues: 866 helix: 1.96 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -2.47 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 632 HIS 0.004 0.001 HIS B 79 PHE 0.020 0.001 PHE B 293 TYR 0.011 0.001 TYR A 436 ARG 0.002 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 180 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8329 (mt0) cc_final: 0.8006 (tm-30) REVERT: B 85 ARG cc_start: 0.8723 (mmt180) cc_final: 0.7719 (mmm160) REVERT: B 195 MET cc_start: 0.7812 (mtp) cc_final: 0.7593 (mtp) REVERT: B 197 LEU cc_start: 0.9232 (tp) cc_final: 0.8821 (tp) REVERT: B 318 TRP cc_start: 0.6469 (t-100) cc_final: 0.5608 (t-100) REVERT: A 423 ASN cc_start: 0.8317 (p0) cc_final: 0.7000 (t0) REVERT: A 465 LYS cc_start: 0.7201 (mptt) cc_final: 0.6733 (tptt) REVERT: A 620 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.7046 (tm-30) outliers start: 25 outliers final: 13 residues processed: 194 average time/residue: 0.1672 time to fit residues: 45.3762 Evaluate side-chains 172 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 158 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 620 GLN Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 682 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN ** A 638 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 7437 Z= 0.242 Angle : 0.661 10.462 10065 Z= 0.334 Chirality : 0.042 0.309 1106 Planarity : 0.004 0.056 1257 Dihedral : 4.244 26.368 973 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.81 % Allowed : 21.45 % Favored : 74.75 % 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: 1.43 (0.29), residues: 866 helix: 1.92 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -2.49 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 541 HIS 0.003 0.001 HIS B 79 PHE 0.035 0.002 PHE B 147 TYR 0.015 0.001 TYR A 436 ARG 0.006 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8399 (mt0) cc_final: 0.8021 (tm-30) REVERT: B 75 ARG cc_start: 0.7475 (ptm-80) cc_final: 0.7207 (ptp90) REVERT: B 78 GLU cc_start: 0.8266 (pt0) cc_final: 0.7931 (pt0) REVERT: B 85 ARG cc_start: 0.8706 (mmt180) cc_final: 0.7752 (mmm160) REVERT: B 195 MET cc_start: 0.7918 (mtp) cc_final: 0.7658 (mtp) REVERT: B 197 LEU cc_start: 0.9254 (tp) cc_final: 0.8862 (tp) REVERT: B 298 MET cc_start: 0.8741 (mtm) cc_final: 0.8221 (mtt) REVERT: B 318 TRP cc_start: 0.6466 (t-100) cc_final: 0.5650 (t-100) REVERT: A 74 TYR cc_start: 0.7973 (t80) cc_final: 0.7640 (t80) REVERT: A 248 GLU cc_start: 0.7622 (mp0) cc_final: 0.7210 (mp0) REVERT: A 423 ASN cc_start: 0.8318 (p0) cc_final: 0.7048 (t0) outliers start: 30 outliers final: 20 residues processed: 179 average time/residue: 0.1750 time to fit residues: 44.0745 Evaluate side-chains 175 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 155 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 633 ASN Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 671 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 0.0040 chunk 62 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 47 optimal weight: 0.2980 chunk 84 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 39 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN A 633 ASN A 638 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7437 Z= 0.175 Angle : 0.652 11.013 10065 Z= 0.325 Chirality : 0.041 0.305 1106 Planarity : 0.004 0.054 1257 Dihedral : 4.135 26.507 973 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.17 % Allowed : 24.24 % Favored : 72.59 % 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: 1.65 (0.29), residues: 866 helix: 2.06 (0.20), residues: 663 sheet: None (None), residues: 0 loop : -2.36 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 632 HIS 0.003 0.001 HIS A 392 PHE 0.038 0.001 PHE B 147 TYR 0.015 0.001 TYR A 90 ARG 0.002 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8318 (mt0) cc_final: 0.8088 (tm-30) REVERT: B 75 ARG cc_start: 0.7420 (ptm-80) cc_final: 0.7205 (ptp90) REVERT: B 78 GLU cc_start: 0.8245 (pt0) cc_final: 0.7875 (pt0) REVERT: B 85 ARG cc_start: 0.8620 (mmt180) cc_final: 0.7670 (mmm160) REVERT: B 197 LEU cc_start: 0.9199 (tp) cc_final: 0.8899 (tp) REVERT: B 298 MET cc_start: 0.8678 (mtm) cc_final: 0.8383 (mtt) REVERT: B 318 TRP cc_start: 0.6382 (t-100) cc_final: 0.5511 (t-100) REVERT: A 74 TYR cc_start: 0.7925 (t80) cc_final: 0.7545 (t80) REVERT: A 465 LYS cc_start: 0.7284 (mptt) cc_final: 0.6777 (tptt) outliers start: 25 outliers final: 17 residues processed: 179 average time/residue: 0.1603 time to fit residues: 40.4114 Evaluate side-chains 170 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 153 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 633 ASN Chi-restraints excluded: chain A residue 638 HIS Chi-restraints excluded: chain A residue 639 GLU Chi-restraints excluded: chain A residue 671 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 81 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 633 ASN A 638 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7437 Z= 0.190 Angle : 0.691 10.974 10065 Z= 0.348 Chirality : 0.041 0.300 1106 Planarity : 0.004 0.052 1257 Dihedral : 4.141 28.187 973 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.66 % Allowed : 25.38 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.29), residues: 866 helix: 2.22 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -2.32 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 305 HIS 0.003 0.001 HIS A 638 PHE 0.047 0.002 PHE B 147 TYR 0.016 0.001 TYR A 90 ARG 0.002 0.000 ARG B 75 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8327 (mt0) cc_final: 0.8082 (tm-30) REVERT: B 75 ARG cc_start: 0.7426 (ptm-80) cc_final: 0.7161 (ptp90) REVERT: B 78 GLU cc_start: 0.8221 (pt0) cc_final: 0.7853 (pt0) REVERT: B 85 ARG cc_start: 0.8542 (mmt180) cc_final: 0.7654 (mmm160) REVERT: B 197 LEU cc_start: 0.9184 (tp) cc_final: 0.8943 (tp) REVERT: B 298 MET cc_start: 0.8689 (mtm) cc_final: 0.8478 (mtt) REVERT: B 318 TRP cc_start: 0.6343 (t-100) cc_final: 0.5498 (t-100) REVERT: A 74 TYR cc_start: 0.7903 (t80) cc_final: 0.7507 (t80) REVERT: A 465 LYS cc_start: 0.7323 (mptt) cc_final: 0.6776 (tptt) outliers start: 21 outliers final: 16 residues processed: 171 average time/residue: 0.1608 time to fit residues: 38.5680 Evaluate side-chains 160 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 144 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 633 ASN Chi-restraints excluded: chain A residue 638 HIS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 682 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.0980 chunk 81 optimal weight: 3.9990 chunk 47 optimal weight: 0.3980 chunk 34 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN A 638 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7437 Z= 0.183 Angle : 0.715 11.909 10065 Z= 0.354 Chirality : 0.041 0.324 1106 Planarity : 0.004 0.051 1257 Dihedral : 4.105 28.732 973 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.79 % Allowed : 26.02 % Favored : 71.19 % 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: 1.83 (0.29), residues: 866 helix: 2.21 (0.20), residues: 659 sheet: None (None), residues: 0 loop : -2.26 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 632 HIS 0.007 0.001 HIS A 638 PHE 0.037 0.001 PHE B 147 TYR 0.015 0.001 TYR A 90 ARG 0.001 0.000 ARG A 535 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8280 (mt0) cc_final: 0.8036 (tm-30) REVERT: B 75 ARG cc_start: 0.7430 (ptm-80) cc_final: 0.7153 (ptp90) REVERT: B 85 ARG cc_start: 0.8638 (mmt180) cc_final: 0.7731 (mmm160) REVERT: B 197 LEU cc_start: 0.9122 (tp) cc_final: 0.8762 (tp) REVERT: B 318 TRP cc_start: 0.6222 (t-100) cc_final: 0.5373 (t-100) REVERT: A 74 TYR cc_start: 0.7889 (t80) cc_final: 0.7498 (t80) REVERT: A 340 CYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7617 (t) REVERT: A 465 LYS cc_start: 0.7293 (mptt) cc_final: 0.6729 (tptt) outliers start: 22 outliers final: 17 residues processed: 163 average time/residue: 0.1644 time to fit residues: 37.9900 Evaluate side-chains 165 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 147 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 631 ILE Chi-restraints excluded: chain A residue 633 ASN Chi-restraints excluded: chain A residue 638 HIS Chi-restraints excluded: chain A residue 671 LEU Chi-restraints excluded: chain A residue 682 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 2.9990 chunk 39 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN A 633 ASN A 638 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7437 Z= 0.237 Angle : 0.742 12.054 10065 Z= 0.371 Chirality : 0.043 0.314 1106 Planarity : 0.004 0.051 1257 Dihedral : 4.202 28.007 973 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.79 % Allowed : 25.89 % Favored : 71.32 % 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: 1.71 (0.29), residues: 866 helix: 2.14 (0.20), residues: 659 sheet: None (None), residues: 0 loop : -2.36 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.004 0.001 HIS A 638 PHE 0.032 0.002 PHE B 147 TYR 0.014 0.001 TYR A 436 ARG 0.002 0.000 ARG B 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1732 Ramachandran restraints generated. 866 Oldfield, 0 Emsley, 866 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 152 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 9 GLN cc_start: 0.8346 (mt0) cc_final: 0.8077 (tm-30) REVERT: B 75 ARG cc_start: 0.7448 (ptm-80) cc_final: 0.7092 (ptp90) REVERT: B 85 ARG cc_start: 0.8579 (mmt180) cc_final: 0.7737 (mmm160) REVERT: B 103 ARG cc_start: 0.5989 (mpp80) cc_final: 0.4021 (ttp-170) REVERT: B 191 MET cc_start: 0.7807 (tmm) cc_final: 0.7181 (tpp) REVERT: B 197 LEU cc_start: 0.9142 (tp) cc_final: 0.8798 (tp) REVERT: B 318 TRP cc_start: 0.6284 (t-100) cc_final: 0.5467 (t-100) REVERT: A 74 TYR cc_start: 0.7938 (t80) cc_final: 0.7641 (t80) REVERT: A 340 CYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7675 (t) REVERT: A 465 LYS cc_start: 0.7361 (mptt) cc_final: 0.6757 (tptt) REVERT: A 534 ASP cc_start: 0.7995 (t70) cc_final: 0.7679 (t0) outliers start: 22 outliers final: 19 residues processed: 165 average time/residue: 0.1648 time to fit residues: 37.8793 Evaluate side-chains 169 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 149 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 170 ASP Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 372 CYS Chi-restraints excluded: chain A residue 402 LEU Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain A residue 633 ASN Chi-restraints excluded: chain A residue 638 HIS Chi-restraints excluded: chain A residue 671 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 29 optimal weight: 0.0040 chunk 71 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 633 ASN A 638 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.153705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.121995 restraints weight = 12782.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.121316 restraints weight = 12038.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.122758 restraints weight = 10231.194| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7437 Z= 0.249 Angle : 0.765 12.178 10065 Z= 0.380 Chirality : 0.044 0.321 1106 Planarity : 0.004 0.051 1257 Dihedral : 4.281 28.465 973 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.17 % Allowed : 26.14 % Favored : 70.69 % 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: 1.59 (0.29), residues: 866 helix: 2.05 (0.20), residues: 659 sheet: None (None), residues: 0 loop : -2.41 (0.40), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.003 0.001 HIS B 122 PHE 0.046 0.002 PHE B 277 TYR 0.014 0.001 TYR A 636 ARG 0.002 0.000 ARG B 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1644.62 seconds wall clock time: 31 minutes 4.68 seconds (1864.68 seconds total)