Starting phenix.real_space_refine on Mon Sep 23 22:29:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhm_34804/09_2024/8hhm_34804.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhm_34804/09_2024/8hhm_34804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhm_34804/09_2024/8hhm_34804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhm_34804/09_2024/8hhm_34804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhm_34804/09_2024/8hhm_34804.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhm_34804/09_2024/8hhm_34804.cif" } resolution = 3.08 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 ------------------------------------------------------------------------------- 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= -0.010 sd= 0.185 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 72 5.49 5 Mg 1 5.21 5 S 18 5.16 5 C 3200 2.51 5 N 1049 2.21 5 O 1217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5558 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 871 Classifications: {'RNA': 40} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pur': 23, 'rna3p_pyr': 12} Link IDs: {'rna2p': 5, 'rna3p': 34} Chain: "C" Number of atoms: 420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 420 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 206 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "A" Number of atoms: 4036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4036 Classifications: {'peptide': 516} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 493} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p_pur': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5229 SG CYS A 552 87.653 21.706 13.199 1.00189.35 S ATOM 5362 SG CYS A 569 85.401 19.773 12.366 1.00191.57 S ATOM 5380 SG CYS A 572 87.817 17.121 13.902 1.00192.17 S Time building chain proxies: 4.06, per 1000 atoms: 0.73 Number of scatterers: 5558 At special positions: 0 Unit cell: (99.932, 84.826, 80.178, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 18 16.00 P 72 15.00 Mg 1 11.99 O 1217 8.00 N 1049 7.00 C 3200 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.67 Conformation dependent library (CDL) restraints added in 886.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 601 " pdb="ZN ZN A 601 " - pdb=" ND1 HIS A 549 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 552 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 569 " pdb="ZN ZN A 601 " - pdb=" SG CYS A 572 " Number of angles added : 3 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 4 sheets defined 50.8% alpha, 16.3% beta 31 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 18 through 51 Processing helix chain 'A' and resid 122 through 145 Processing helix chain 'A' and resid 151 through 176 Processing helix chain 'A' and resid 206 through 212 removed outlier: 3.549A pdb=" N ASP A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 235 removed outlier: 3.802A pdb=" N GLN A 234 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 Processing helix chain 'A' and resid 363 through 397 Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 417 through 428 removed outlier: 4.117A pdb=" N PHE A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 479 removed outlier: 3.770A pdb=" N ASP A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 445 " --> pdb=" O ALA A 441 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 508 through 518 removed outlier: 3.895A pdb=" N ARG A 514 " --> pdb=" O ILE A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 533 removed outlier: 3.593A pdb=" N LEU A 522 " --> pdb=" O ALA A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 4.187A pdb=" N SER A 564 " --> pdb=" O ARG A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 591 Processing sheet with id=AA1, first strand: chain 'A' and resid 190 through 195 removed outlier: 6.714A pdb=" N ILE A 278 " --> pdb=" O ARG A 301 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ARG A 301 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY A 280 " --> pdb=" O THR A 299 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ALA A 294 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY A 10 " --> pdb=" O GLN A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 322 through 323 removed outlier: 6.570A pdb=" N ILE A 359 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N THR A 331 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY A 357 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 323 removed outlier: 3.950A pdb=" N ASP A 485 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU A 318 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL A 482 " --> pdb=" O THR A 538 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N VAL A 540 " --> pdb=" O VAL A 482 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N VAL A 484 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 567 through 568 242 hydrogen bonds defined for protein. 705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 80 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 31 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 1.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1314 1.33 - 1.45: 1544 1.45 - 1.57: 2794 1.57 - 1.69: 140 1.69 - 1.81: 29 Bond restraints: 5821 Sorted by residual: bond pdb=" N THR A 3 " pdb=" CA THR A 3 " ideal model delta sigma weight residual 1.466 1.452 0.015 1.36e-02 5.41e+03 1.21e+00 bond pdb=" CA HIS A 463 " pdb=" C HIS A 463 " ideal model delta sigma weight residual 1.524 1.512 0.012 1.32e-02 5.74e+03 8.43e-01 bond pdb=" C MET A 9 " pdb=" N GLY A 10 " ideal model delta sigma weight residual 1.332 1.328 0.004 5.00e-03 4.00e+04 8.08e-01 bond pdb=" C3' DG D 23 " pdb=" O3' DG D 23 " ideal model delta sigma weight residual 1.422 1.448 -0.026 3.00e-02 1.11e+03 7.80e-01 bond pdb=" CG1 ILE A 278 " pdb=" CD1 ILE A 278 " ideal model delta sigma weight residual 1.513 1.480 0.033 3.90e-02 6.57e+02 6.96e-01 ... (remaining 5816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 7926 1.21 - 2.42: 265 2.42 - 3.64: 36 3.64 - 4.85: 5 4.85 - 6.06: 2 Bond angle restraints: 8234 Sorted by residual: angle pdb=" C VAL A 329 " pdb=" N ALA A 330 " pdb=" CA ALA A 330 " ideal model delta sigma weight residual 121.75 117.77 3.98 1.73e+00 3.34e-01 5.29e+00 angle pdb=" N VAL A 329 " pdb=" CA VAL A 329 " pdb=" C VAL A 329 " ideal model delta sigma weight residual 109.34 113.63 -4.29 2.08e+00 2.31e-01 4.25e+00 angle pdb=" CA VAL A 329 " pdb=" C VAL A 329 " pdb=" N ALA A 330 " ideal model delta sigma weight residual 116.60 119.57 -2.97 1.45e+00 4.76e-01 4.19e+00 angle pdb=" C1' G B -27 " pdb=" N9 G B -27 " pdb=" C4 G B -27 " ideal model delta sigma weight residual 126.50 132.56 -6.06 3.00e+00 1.11e-01 4.08e+00 angle pdb=" C GLN A 453 " pdb=" N GLU A 454 " pdb=" CA GLU A 454 " ideal model delta sigma weight residual 121.80 117.46 4.34 2.16e+00 2.14e-01 4.04e+00 ... (remaining 8229 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.76: 2753 15.76 - 31.52: 353 31.52 - 47.28: 200 47.28 - 63.03: 106 63.03 - 78.79: 45 Dihedral angle restraints: 3457 sinusoidal: 1965 harmonic: 1492 Sorted by residual: dihedral pdb=" O4' G B -11 " pdb=" C1' G B -11 " pdb=" N9 G B -11 " pdb=" C4 G B -11 " ideal model delta sinusoidal sigma weight residual -106.00 -168.18 62.18 1 1.70e+01 3.46e-03 1.77e+01 dihedral pdb=" CG ARG A 513 " pdb=" CD ARG A 513 " pdb=" NE ARG A 513 " pdb=" CZ ARG A 513 " ideal model delta sinusoidal sigma weight residual 180.00 136.03 43.97 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CA ASP A 477 " pdb=" CB ASP A 477 " pdb=" CG ASP A 477 " pdb=" OD1 ASP A 477 " ideal model delta sinusoidal sigma weight residual -30.00 -84.88 54.88 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 3454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 567 0.026 - 0.052: 247 0.052 - 0.077: 90 0.077 - 0.103: 30 0.103 - 0.129: 17 Chirality restraints: 951 Sorted by residual: chirality pdb=" CA ILE A 359 " pdb=" N ILE A 359 " pdb=" C ILE A 359 " pdb=" CB ILE A 359 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA VAL A 361 " pdb=" N VAL A 361 " pdb=" C VAL A 361 " pdb=" CB VAL A 361 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.46e-01 ... (remaining 948 not shown) Planarity restraints: 803 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 452 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.05e+00 pdb=" C GLN A 452 " -0.039 2.00e-02 2.50e+03 pdb=" O GLN A 452 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 453 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 468 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.83e+00 pdb=" C TYR A 468 " 0.029 2.00e-02 2.50e+03 pdb=" O TYR A 468 " -0.011 2.00e-02 2.50e+03 pdb=" N ARG A 469 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 462 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.42e+00 pdb=" C GLY A 462 " 0.027 2.00e-02 2.50e+03 pdb=" O GLY A 462 " -0.010 2.00e-02 2.50e+03 pdb=" N HIS A 463 " -0.009 2.00e-02 2.50e+03 ... (remaining 800 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 140 2.66 - 3.22: 5023 3.22 - 3.78: 9599 3.78 - 4.34: 12510 4.34 - 4.90: 19151 Nonbonded interactions: 46423 Sorted by model distance: nonbonded pdb=" OP1 G B -22 " pdb="MG MG B 101 " model vdw 2.106 2.170 nonbonded pdb=" OG1 THR A 3 " pdb=" OD1 ASP A 304 " model vdw 2.210 3.040 nonbonded pdb=" O TRP A 428 " pdb=" OG SER A 436 " model vdw 2.228 3.040 nonbonded pdb=" OG SER A 334 " pdb=" O ALA A 336 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR A 468 " pdb=" O ALA A 517 " model vdw 2.305 3.040 ... (remaining 46418 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.060 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 20.180 Find NCS groups from input model: 0.060 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5821 Z= 0.287 Angle : 0.534 6.058 8234 Z= 0.300 Chirality : 0.036 0.129 951 Planarity : 0.005 0.030 803 Dihedral : 20.700 78.793 2489 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.34 % Allowed : 12.65 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.39), residues: 510 helix: 1.71 (0.34), residues: 252 sheet: 0.63 (0.63), residues: 81 loop : -0.24 (0.46), residues: 177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 440 HIS 0.003 0.001 HIS A 269 PHE 0.013 0.002 PHE A 582 TYR 0.009 0.001 TYR A 217 ARG 0.003 0.000 ARG A 245 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.8183 (mmt) cc_final: 0.7952 (mpp) REVERT: A 19 GLU cc_start: 0.8336 (tp30) cc_final: 0.7901 (tp30) REVERT: A 46 LEU cc_start: 0.7829 (mt) cc_final: 0.7523 (mt) REVERT: A 127 LYS cc_start: 0.9246 (tppt) cc_final: 0.9007 (tppt) REVERT: A 327 THR cc_start: 0.8918 (m) cc_final: 0.8522 (m) REVERT: A 340 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8897 (mm) REVERT: A 370 THR cc_start: 0.8726 (m) cc_final: 0.8350 (p) REVERT: A 408 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8651 (mm-30) REVERT: A 563 LEU cc_start: 0.8523 (mt) cc_final: 0.8307 (mm) outliers start: 14 outliers final: 5 residues processed: 104 average time/residue: 0.2771 time to fit residues: 34.1220 Evaluate side-chains 65 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 374 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5821 Z= 0.208 Angle : 0.532 9.514 8234 Z= 0.290 Chirality : 0.035 0.135 951 Planarity : 0.005 0.040 803 Dihedral : 21.968 78.478 1564 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.58 % Allowed : 15.99 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.90 (0.39), residues: 510 helix: 2.36 (0.33), residues: 260 sheet: 1.37 (0.64), residues: 69 loop : -0.45 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 440 HIS 0.002 0.001 HIS A 7 PHE 0.007 0.001 PHE A 582 TYR 0.020 0.002 TYR A 576 ARG 0.008 0.001 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 68 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8119 (mmt) cc_final: 0.7861 (mpp) REVERT: A 340 ILE cc_start: 0.9261 (OUTLIER) cc_final: 0.8880 (mm) REVERT: A 394 LEU cc_start: 0.8511 (tp) cc_final: 0.8106 (pp) REVERT: A 408 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8493 (mm-30) REVERT: A 415 TRP cc_start: 0.7114 (m-10) cc_final: 0.6793 (m-10) REVERT: A 433 THR cc_start: 0.7407 (p) cc_final: 0.7206 (p) REVERT: A 530 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8119 (mmm) REVERT: A 555 VAL cc_start: 0.6949 (OUTLIER) cc_final: 0.6482 (m) outliers start: 15 outliers final: 9 residues processed: 81 average time/residue: 0.2372 time to fit residues: 23.5611 Evaluate side-chains 59 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 581 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 14 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 452 GLN A 478 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5821 Z= 0.214 Angle : 0.515 8.345 8234 Z= 0.280 Chirality : 0.035 0.131 951 Planarity : 0.004 0.044 803 Dihedral : 21.853 78.227 1561 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.10 % Allowed : 17.42 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.02 (0.38), residues: 510 helix: 2.52 (0.33), residues: 260 sheet: 1.75 (0.64), residues: 67 loop : -0.62 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 442 HIS 0.008 0.001 HIS A 317 PHE 0.008 0.001 PHE A 582 TYR 0.018 0.002 TYR A 576 ARG 0.016 0.001 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 53 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8126 (mmt) cc_final: 0.7859 (mpp) REVERT: A 127 LYS cc_start: 0.9102 (tppt) cc_final: 0.8873 (ttpp) REVERT: A 177 LYS cc_start: 0.8127 (mmmm) cc_final: 0.7782 (tptp) REVERT: A 340 ILE cc_start: 0.9274 (OUTLIER) cc_final: 0.8893 (mm) REVERT: A 394 LEU cc_start: 0.8476 (tp) cc_final: 0.8135 (pp) REVERT: A 408 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8458 (mm-30) REVERT: A 530 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8363 (mmp) REVERT: A 586 MET cc_start: 0.8128 (mmm) cc_final: 0.7913 (mmm) outliers start: 13 outliers final: 6 residues processed: 62 average time/residue: 0.2801 time to fit residues: 20.9805 Evaluate side-chains 54 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 530 MET Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 581 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 52 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 5821 Z= 0.295 Angle : 0.553 8.149 8234 Z= 0.299 Chirality : 0.037 0.166 951 Planarity : 0.005 0.035 803 Dihedral : 21.819 78.601 1558 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 4.30 % Allowed : 16.95 % Favored : 78.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.38), residues: 510 helix: 2.38 (0.32), residues: 260 sheet: 1.66 (0.64), residues: 67 loop : -0.76 (0.43), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 440 HIS 0.008 0.001 HIS A 317 PHE 0.007 0.001 PHE A 582 TYR 0.018 0.002 TYR A 576 ARG 0.008 0.001 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 58 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8190 (mmt) cc_final: 0.7928 (mpp) REVERT: A 46 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7451 (mm) REVERT: A 127 LYS cc_start: 0.9120 (tppt) cc_final: 0.8877 (ttpp) REVERT: A 340 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.8896 (mm) REVERT: A 394 LEU cc_start: 0.8431 (tp) cc_final: 0.8109 (pp) REVERT: A 408 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8477 (mm-30) REVERT: A 563 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8239 (mm) outliers start: 18 outliers final: 9 residues processed: 72 average time/residue: 0.2681 time to fit residues: 23.4429 Evaluate side-chains 62 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 50 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 581 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 41 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 50 optimal weight: 30.0000 chunk 14 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5821 Z= 0.223 Angle : 0.521 7.399 8234 Z= 0.281 Chirality : 0.036 0.172 951 Planarity : 0.005 0.045 803 Dihedral : 21.806 78.253 1558 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.49 % Allowed : 17.18 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.38), residues: 510 helix: 2.46 (0.33), residues: 260 sheet: 1.66 (0.64), residues: 67 loop : -0.65 (0.44), residues: 183 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 442 HIS 0.007 0.001 HIS A 317 PHE 0.005 0.001 PHE A 582 TYR 0.019 0.002 TYR A 576 ARG 0.008 0.001 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 54 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.8122 (mmt) cc_final: 0.7892 (mpp) REVERT: A 46 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7528 (mm) REVERT: A 127 LYS cc_start: 0.9103 (tppt) cc_final: 0.8842 (ttpp) REVERT: A 340 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8896 (mm) REVERT: A 394 LEU cc_start: 0.8410 (tp) cc_final: 0.8077 (pp) REVERT: A 408 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8461 (mm-30) outliers start: 23 outliers final: 12 residues processed: 71 average time/residue: 0.2237 time to fit residues: 19.8047 Evaluate side-chains 59 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 587 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 18 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 40 optimal weight: 30.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 5821 Z= 0.476 Angle : 0.655 7.834 8234 Z= 0.348 Chirality : 0.042 0.138 951 Planarity : 0.006 0.064 803 Dihedral : 21.865 79.332 1558 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.49 % Allowed : 17.18 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.45 (0.37), residues: 510 helix: 2.06 (0.32), residues: 261 sheet: 1.31 (0.65), residues: 69 loop : -0.84 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 450 HIS 0.009 0.002 HIS A 317 PHE 0.012 0.002 PHE A 582 TYR 0.017 0.003 TYR A 576 ARG 0.008 0.001 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 45 time to evaluate : 0.528 Fit side-chains REVERT: A 4 MET cc_start: 0.8210 (mmt) cc_final: 0.7982 (mpp) REVERT: A 46 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7428 (mm) REVERT: A 340 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.8757 (mm) REVERT: A 365 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7693 (mm) REVERT: A 394 LEU cc_start: 0.8463 (tp) cc_final: 0.8125 (pp) REVERT: A 408 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8511 (mm-30) outliers start: 23 outliers final: 15 residues processed: 64 average time/residue: 0.2031 time to fit residues: 17.0663 Evaluate side-chains 58 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 40 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 340 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 474 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 587 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 25 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5821 Z= 0.244 Angle : 0.548 7.133 8234 Z= 0.294 Chirality : 0.037 0.194 951 Planarity : 0.005 0.062 803 Dihedral : 21.882 78.586 1558 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.06 % Allowed : 18.38 % Favored : 77.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.38), residues: 510 helix: 2.33 (0.33), residues: 260 sheet: 1.40 (0.63), residues: 69 loop : -0.56 (0.44), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 442 HIS 0.009 0.001 HIS A 317 PHE 0.009 0.001 PHE A 582 TYR 0.020 0.002 TYR A 576 ARG 0.008 0.001 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 52 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.8149 (mmt) cc_final: 0.7938 (mpp) REVERT: A 46 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7550 (mm) REVERT: A 127 LYS cc_start: 0.9045 (tppt) cc_final: 0.8820 (ttpp) REVERT: A 394 LEU cc_start: 0.8426 (tp) cc_final: 0.8109 (pp) REVERT: A 408 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8517 (mm-30) REVERT: A 563 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.8056 (mm) REVERT: A 586 MET cc_start: 0.7950 (mmm) cc_final: 0.7745 (mmt) outliers start: 17 outliers final: 11 residues processed: 66 average time/residue: 0.2213 time to fit residues: 18.4938 Evaluate side-chains 56 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 250 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 587 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 0.3980 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 40 optimal weight: 30.0000 chunk 15 optimal weight: 7.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5821 Z= 0.178 Angle : 0.513 6.746 8234 Z= 0.276 Chirality : 0.035 0.118 951 Planarity : 0.004 0.053 803 Dihedral : 21.727 77.742 1556 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.10 % Allowed : 19.81 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.07 (0.38), residues: 510 helix: 2.46 (0.33), residues: 262 sheet: 1.76 (0.64), residues: 67 loop : -0.45 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 442 HIS 0.007 0.001 HIS A 317 PHE 0.005 0.001 PHE A 582 TYR 0.021 0.001 TYR A 576 ARG 0.009 0.001 ARG A 513 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.531 Fit side-chains REVERT: A 4 MET cc_start: 0.8074 (mmt) cc_final: 0.7830 (mpp) REVERT: A 46 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7557 (mm) REVERT: A 125 ARG cc_start: 0.8720 (mtt180) cc_final: 0.8432 (mtm180) REVERT: A 127 LYS cc_start: 0.8947 (tppt) cc_final: 0.8675 (ttpp) REVERT: A 394 LEU cc_start: 0.8357 (tp) cc_final: 0.8065 (pp) REVERT: A 586 MET cc_start: 0.7878 (mmm) cc_final: 0.7673 (mmt) outliers start: 13 outliers final: 7 residues processed: 59 average time/residue: 0.2368 time to fit residues: 17.4272 Evaluate side-chains 53 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 587 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.8980 chunk 49 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5821 Z= 0.171 Angle : 0.526 7.046 8234 Z= 0.281 Chirality : 0.035 0.120 951 Planarity : 0.004 0.027 803 Dihedral : 21.666 77.470 1556 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.39 % Allowed : 20.29 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.26 (0.38), residues: 510 helix: 2.70 (0.33), residues: 256 sheet: 1.81 (0.65), residues: 67 loop : -0.37 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 415 HIS 0.006 0.001 HIS A 317 PHE 0.010 0.001 PHE A 582 TYR 0.025 0.002 TYR A 576 ARG 0.008 0.000 ARG A 512 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 47 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: A 4 MET cc_start: 0.8071 (mmt) cc_final: 0.7813 (mpp) REVERT: A 46 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7558 (mm) REVERT: A 125 ARG cc_start: 0.8736 (mtt180) cc_final: 0.8426 (mtm180) REVERT: A 127 LYS cc_start: 0.8962 (tppt) cc_final: 0.8677 (ttpp) REVERT: A 394 LEU cc_start: 0.8364 (tp) cc_final: 0.8079 (pp) outliers start: 10 outliers final: 7 residues processed: 55 average time/residue: 0.2285 time to fit residues: 15.7253 Evaluate side-chains 57 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 587 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 4 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 36 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5821 Z= 0.332 Angle : 0.603 7.036 8234 Z= 0.321 Chirality : 0.039 0.131 951 Planarity : 0.005 0.039 803 Dihedral : 21.698 78.324 1556 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.91 % Allowed : 21.00 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.84 (0.38), residues: 510 helix: 2.25 (0.33), residues: 263 sheet: 1.58 (0.64), residues: 69 loop : -0.53 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 415 HIS 0.004 0.001 HIS A 222 PHE 0.013 0.002 PHE A 582 TYR 0.020 0.002 TYR A 576 ARG 0.009 0.001 ARG A 512 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.475 Fit side-chains REVERT: A 4 MET cc_start: 0.8169 (mmt) cc_final: 0.7926 (mpp) REVERT: A 46 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7557 (mm) REVERT: A 125 ARG cc_start: 0.8717 (mtt180) cc_final: 0.8389 (mtm180) REVERT: A 394 LEU cc_start: 0.8339 (tp) cc_final: 0.8053 (pp) REVERT: A 408 GLU cc_start: 0.7926 (mm-30) cc_final: 0.7660 (mm-30) REVERT: A 563 LEU cc_start: 0.8456 (mt) cc_final: 0.8150 (pp) outliers start: 8 outliers final: 6 residues processed: 61 average time/residue: 0.2212 time to fit residues: 16.9127 Evaluate side-chains 50 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 581 SER Chi-restraints excluded: chain A residue 587 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 47 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 0.0170 chunk 40 optimal weight: 40.0000 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 overall best weight: 2.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.139206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.106648 restraints weight = 10782.719| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.38 r_work: 0.3494 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5821 Z= 0.183 Angle : 0.545 6.943 8234 Z= 0.291 Chirality : 0.035 0.123 951 Planarity : 0.004 0.032 803 Dihedral : 21.648 77.640 1556 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.67 % Allowed : 21.96 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.17 (0.38), residues: 510 helix: 2.59 (0.33), residues: 256 sheet: 1.78 (0.63), residues: 67 loop : -0.36 (0.46), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 415 HIS 0.002 0.001 HIS A 317 PHE 0.016 0.001 PHE A 582 TYR 0.021 0.002 TYR A 576 ARG 0.010 0.001 ARG A 512 =============================================================================== Job complete usr+sys time: 1332.81 seconds wall clock time: 24 minutes 18.46 seconds (1458.46 seconds total)