Starting phenix.real_space_refine on Sun Mar 10 22:14:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhm_34804/03_2024/8hhm_34804.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhm_34804/03_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_34804/03_2024/8hhm_34804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhm_34804/03_2024/8hhm_34804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhm_34804/03_2024/8hhm_34804.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hhm_34804/03_2024/8hhm_34804.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 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: 4.02, per 1000 atoms: 0.72 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 - 3.50 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: 3.14 Conformation dependent library (CDL) restraints added in 900.2 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: 2.17 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: 2.31 Time building geometry restraints manager: 2.89 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: 99.67 - 106.54: 555 106.54 - 113.41: 3288 113.41 - 120.27: 2110 120.27 - 127.14: 2051 127.14 - 134.01: 230 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 2.440 nonbonded pdb=" O TRP A 428 " pdb=" OG SER A 436 " model vdw 2.228 2.440 nonbonded pdb=" OG SER A 334 " pdb=" O ALA A 336 " model vdw 2.260 2.440 nonbonded pdb=" OH TYR A 468 " pdb=" O ALA A 517 " model vdw 2.305 2.440 ... (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 ========== 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: 0.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 23.480 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.450 ------------------------------------------------------------------------------- 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 : 0.571 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: 0.2814 time to fit residues: 34.6485 Evaluate side-chains 65 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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: 10.0000 chunk 43 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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: 0.8044 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5821 Z= 0.192 Angle : 0.517 8.836 8234 Z= 0.282 Chirality : 0.035 0.128 951 Planarity : 0.004 0.030 803 Dihedral : 21.946 78.346 1564 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.86 % Allowed : 15.99 % Favored : 81.15 % 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: 2.06 (0.39), residues: 510 helix: 2.49 (0.33), residues: 260 sheet: 1.35 (0.65), residues: 69 loop : -0.31 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 440 HIS 0.002 0.000 HIS A 7 PHE 0.007 0.001 PHE A 582 TYR 0.019 0.002 TYR A 576 ARG 0.008 0.001 ARG A 126 *********************** 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: 12 poor density : 71 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 MET cc_start: 0.8192 (mmt) cc_final: 0.7932 (mpp) REVERT: A 340 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.8884 (mm) REVERT: A 366 GLU cc_start: 0.8536 (mp0) cc_final: 0.8304 (mp0) REVERT: A 370 THR cc_start: 0.8618 (m) cc_final: 0.8394 (p) REVERT: A 394 LEU cc_start: 0.8501 (tp) cc_final: 0.8095 (pp) REVERT: A 555 VAL cc_start: 0.6906 (OUTLIER) cc_final: 0.6160 (m) REVERT: A 563 LEU cc_start: 0.8498 (mt) cc_final: 0.8222 (mm) outliers start: 12 outliers final: 7 residues processed: 81 average time/residue: 0.2470 time to fit residues: 24.5512 Evaluate side-chains 58 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 7.9990 chunk 16 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 35 optimal weight: 0.0060 chunk 14 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5821 Z= 0.174 Angle : 0.496 7.826 8234 Z= 0.269 Chirality : 0.034 0.126 951 Planarity : 0.004 0.028 803 Dihedral : 21.788 78.005 1561 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.43 % Allowed : 18.85 % Favored : 79.71 % 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: 2.22 (0.38), residues: 510 helix: 2.72 (0.33), residues: 260 sheet: 1.39 (0.65), residues: 69 loop : -0.40 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 442 HIS 0.009 0.001 HIS A 317 PHE 0.010 0.001 PHE A 582 TYR 0.019 0.002 TYR A 576 ARG 0.005 0.000 ARG A 126 *********************** 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 69 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 63 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LYS cc_start: 0.9095 (tppt) cc_final: 0.8863 (ttpp) REVERT: A 177 LYS cc_start: 0.8148 (mmmm) cc_final: 0.7797 (tptp) REVERT: A 340 ILE cc_start: 0.9282 (OUTLIER) cc_final: 0.8884 (mm) REVERT: A 394 LEU cc_start: 0.8460 (tp) cc_final: 0.8120 (pp) REVERT: A 408 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7408 (mm-30) REVERT: A 415 TRP cc_start: 0.7380 (m-10) cc_final: 0.6896 (m-10) outliers start: 6 outliers final: 3 residues processed: 68 average time/residue: 0.2518 time to fit residues: 21.0688 Evaluate side-chains 53 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 340 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 27 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 56 optimal weight: 30.0000 chunk 50 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 5.7388 ------------------------------------------------------------------------------- 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: 0.8104 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5821 Z= 0.346 Angle : 0.582 8.262 8234 Z= 0.311 Chirality : 0.038 0.165 951 Planarity : 0.005 0.036 803 Dihedral : 21.809 78.761 1558 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.77 % Allowed : 16.47 % 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: 1.96 (0.38), residues: 510 helix: 2.50 (0.33), residues: 261 sheet: 1.93 (0.66), residues: 65 loop : -0.78 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 440 HIS 0.008 0.001 HIS A 317 PHE 0.011 0.002 PHE A 582 TYR 0.019 0.002 TYR A 576 ARG 0.010 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 72 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 52 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7284 (mm) REVERT: A 127 LYS cc_start: 0.9133 (tppt) cc_final: 0.8895 (ttpp) REVERT: A 177 LYS cc_start: 0.8027 (mmmm) cc_final: 0.7512 (tptp) REVERT: A 340 ILE cc_start: 0.9296 (OUTLIER) cc_final: 0.8927 (mm) REVERT: A 394 LEU cc_start: 0.8534 (tp) cc_final: 0.8167 (pp) REVERT: A 586 MET cc_start: 0.7850 (mtt) cc_final: 0.7570 (mtm) outliers start: 20 outliers final: 13 residues processed: 67 average time/residue: 0.2476 time to fit residues: 20.3588 Evaluate side-chains 64 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 157 THR 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 323 THR 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 374 ASN 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: 5.9990 chunk 47 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 50 optimal weight: 30.0000 chunk 14 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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: 0.8099 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 5821 Z= 0.295 Angle : 0.545 7.772 8234 Z= 0.292 Chirality : 0.037 0.129 951 Planarity : 0.005 0.052 803 Dihedral : 21.864 78.718 1558 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 5.25 % Allowed : 17.42 % 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: 1.85 (0.38), residues: 510 helix: 2.39 (0.33), residues: 263 sheet: 1.89 (0.65), residues: 65 loop : -0.85 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 442 HIS 0.007 0.001 HIS A 317 PHE 0.008 0.001 PHE A 582 TYR 0.019 0.002 TYR A 576 ARG 0.004 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 75 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 53 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7535 (mm) REVERT: A 127 LYS cc_start: 0.9142 (tppt) cc_final: 0.8885 (ttpp) REVERT: A 177 LYS cc_start: 0.8055 (mmmm) cc_final: 0.7561 (tptp) REVERT: A 340 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8961 (mm) REVERT: A 394 LEU cc_start: 0.8425 (tp) cc_final: 0.8089 (pp) REVERT: A 530 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8291 (mmp) REVERT: A 563 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8226 (mm) outliers start: 22 outliers final: 14 residues processed: 70 average time/residue: 0.2357 time to fit residues: 20.4368 Evaluate side-chains 68 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 50 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 125 ARG Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 THR 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 323 THR 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 485 ASP Chi-restraints excluded: chain A residue 530 MET 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 13 optimal weight: 7.9990 chunk 56 optimal weight: 0.0870 chunk 46 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 40 optimal weight: 50.0000 overall best weight: 3.2166 ------------------------------------------------------------------------------- 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: 0.8083 moved from start: 0.2581 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= 0.209 Angle : 0.509 7.220 8234 Z= 0.273 Chirality : 0.035 0.120 951 Planarity : 0.004 0.035 803 Dihedral : 21.831 78.346 1558 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.30 % Allowed : 19.33 % 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: 1.96 (0.38), residues: 510 helix: 2.53 (0.33), residues: 263 sheet: 1.70 (0.65), residues: 67 loop : -0.80 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 320 HIS 0.009 0.001 HIS A 317 PHE 0.011 0.001 PHE A 582 TYR 0.020 0.002 TYR A 576 ARG 0.007 0.001 ARG A 126 *********************** 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 71 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 53 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7305 (mm) REVERT: A 127 LYS cc_start: 0.9110 (tppt) cc_final: 0.8840 (ttpp) REVERT: A 177 LYS cc_start: 0.8019 (mmmm) cc_final: 0.7557 (tptp) REVERT: A 340 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.8957 (mm) REVERT: A 394 LEU cc_start: 0.8406 (tp) cc_final: 0.8080 (pp) REVERT: A 563 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8108 (mm) REVERT: A 586 MET cc_start: 0.7501 (mtm) cc_final: 0.7231 (mtt) outliers start: 18 outliers final: 12 residues processed: 66 average time/residue: 0.2430 time to fit residues: 19.7998 Evaluate side-chains 65 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 50 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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 125 ARG Chi-restraints excluded: chain A residue 147 ASP Chi-restraints excluded: chain A residue 157 THR 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 323 THR 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 31 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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: 0.8050 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5821 Z= 0.152 Angle : 0.480 6.897 8234 Z= 0.258 Chirality : 0.034 0.123 951 Planarity : 0.004 0.027 803 Dihedral : 21.726 77.580 1558 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.63 % Allowed : 20.76 % Favored : 76.61 % 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: 2.22 (0.38), residues: 510 helix: 2.71 (0.33), residues: 263 sheet: 1.79 (0.65), residues: 67 loop : -0.60 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 320 HIS 0.006 0.001 HIS A 317 PHE 0.007 0.001 PHE A 582 TYR 0.021 0.001 TYR A 576 ARG 0.005 0.000 ARG A 126 *********************** 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 61 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 50 time to evaluate : 0.498 Fit side-chains REVERT: A 46 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7455 (mm) REVERT: A 127 LYS cc_start: 0.9011 (tppt) cc_final: 0.8753 (ttpp) REVERT: A 177 LYS cc_start: 0.7995 (mmmm) cc_final: 0.7581 (tptp) REVERT: A 394 LEU cc_start: 0.8358 (tp) cc_final: 0.8048 (pp) REVERT: A 457 ARG cc_start: 0.8401 (ttm-80) cc_final: 0.7951 (mtm110) REVERT: A 563 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8044 (mm) REVERT: A 586 MET cc_start: 0.7387 (mtm) cc_final: 0.7117 (mtt) outliers start: 11 outliers final: 5 residues processed: 58 average time/residue: 0.2610 time to fit residues: 18.6090 Evaluate side-chains 53 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 46 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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 323 THR Chi-restraints excluded: chain A residue 365 ILE 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: 0.2980 chunk 5 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 50 optimal weight: 30.0000 chunk 53 optimal weight: 20.0000 chunk 48 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 40 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 overall best weight: 2.1784 ------------------------------------------------------------------------------- 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: 0.8052 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5821 Z= 0.164 Angle : 0.496 6.678 8234 Z= 0.266 Chirality : 0.034 0.121 951 Planarity : 0.004 0.029 803 Dihedral : 21.667 77.534 1556 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: 2.19 (0.38), residues: 510 helix: 2.67 (0.33), residues: 263 sheet: 1.77 (0.66), residues: 67 loop : -0.58 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 320 HIS 0.006 0.001 HIS A 317 PHE 0.012 0.001 PHE A 582 TYR 0.021 0.001 TYR A 576 ARG 0.007 0.000 ARG A 512 *********************** 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 64 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7397 (mm) REVERT: A 125 ARG cc_start: 0.8694 (mtt180) cc_final: 0.8341 (ptp-170) REVERT: A 127 LYS cc_start: 0.8965 (tppt) cc_final: 0.8685 (ttpp) REVERT: A 177 LYS cc_start: 0.8002 (mmmm) cc_final: 0.7592 (tptp) REVERT: A 394 LEU cc_start: 0.8352 (tp) cc_final: 0.8044 (pp) REVERT: A 457 ARG cc_start: 0.8422 (ttm-80) cc_final: 0.7967 (mtm110) REVERT: A 586 MET cc_start: 0.7358 (mtm) cc_final: 0.7099 (mtt) outliers start: 13 outliers final: 8 residues processed: 60 average time/residue: 0.2482 time to fit residues: 18.4964 Evaluate side-chains 56 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 47 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 194 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 323 THR 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: 7.9990 chunk 34 optimal weight: 0.0070 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 overall best weight: 2.3602 ------------------------------------------------------------------------------- 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: 0.8053 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5821 Z= 0.174 Angle : 0.518 8.306 8234 Z= 0.276 Chirality : 0.034 0.121 951 Planarity : 0.004 0.028 803 Dihedral : 21.633 77.413 1556 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.63 % Allowed : 20.76 % Favored : 76.61 % 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: 2.10 (0.38), residues: 510 helix: 2.67 (0.33), residues: 263 sheet: 1.39 (0.73), residues: 55 loop : -0.46 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.002 TRP A 320 HIS 0.002 0.001 HIS A 317 PHE 0.009 0.001 PHE A 582 TYR 0.023 0.002 TYR A 402 ARG 0.007 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 68 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7376 (mm) REVERT: A 127 LYS cc_start: 0.8918 (tppt) cc_final: 0.8631 (ttpp) REVERT: A 177 LYS cc_start: 0.7996 (mmmm) cc_final: 0.7680 (tptp) REVERT: A 394 LEU cc_start: 0.8341 (tp) cc_final: 0.8040 (pp) REVERT: A 408 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7409 (mm-30) REVERT: A 457 ARG cc_start: 0.8427 (ttm-80) cc_final: 0.7974 (mtm110) REVERT: A 586 MET cc_start: 0.7391 (mtm) cc_final: 0.7134 (mtt) outliers start: 11 outliers final: 9 residues processed: 67 average time/residue: 0.2207 time to fit residues: 18.6643 Evaluate side-chains 58 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 48 time to evaluate : 0.524 ------------------------------------------------------------------------------- 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 308 VAL 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: 30.0000 chunk 28 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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: 0.8097 moved from start: 0.2998 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= 0.285 Angle : 0.576 8.902 8234 Z= 0.307 Chirality : 0.037 0.123 951 Planarity : 0.005 0.069 803 Dihedral : 21.661 77.947 1556 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.15 % Allowed : 21.00 % Favored : 76.85 % 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: 1.87 (0.38), residues: 510 helix: 2.46 (0.33), residues: 263 sheet: 1.09 (0.73), residues: 57 loop : -0.49 (0.43), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 415 HIS 0.005 0.001 HIS A 516 PHE 0.014 0.001 PHE A 582 TYR 0.019 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 57 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.641 Fit side-chains REVERT: A 46 LEU cc_start: 0.7688 (OUTLIER) cc_final: 0.7344 (mm) REVERT: A 125 ARG cc_start: 0.8722 (mtt180) cc_final: 0.8433 (mtm180) REVERT: A 177 LYS cc_start: 0.7930 (mmmm) cc_final: 0.7618 (tptp) REVERT: A 325 GLU cc_start: 0.7900 (mp0) cc_final: 0.7673 (mt-10) REVERT: A 394 LEU cc_start: 0.8369 (tp) cc_final: 0.8066 (pp) REVERT: A 457 ARG cc_start: 0.8491 (ttm-80) cc_final: 0.8004 (mtm110) REVERT: A 586 MET cc_start: 0.7508 (mtm) cc_final: 0.7213 (mtt) outliers start: 9 outliers final: 7 residues processed: 56 average time/residue: 0.2421 time to fit residues: 16.8898 Evaluate side-chains 54 residues out of total 419 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 5 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 40 optimal weight: 50.0000 chunk 2 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.136548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.103114 restraints weight = 11017.119| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 2.40 r_work: 0.3441 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 5821 Z= 0.310 Angle : 0.601 11.033 8234 Z= 0.319 Chirality : 0.037 0.121 951 Planarity : 0.005 0.061 803 Dihedral : 21.743 78.266 1556 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.63 % Allowed : 20.76 % Favored : 76.61 % 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: 1.91 (0.38), residues: 510 helix: 2.36 (0.33), residues: 263 sheet: 1.16 (0.62), residues: 80 loop : -0.47 (0.46), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 415 HIS 0.003 0.001 HIS A 549 PHE 0.016 0.002 PHE A 582 TYR 0.019 0.002 TYR A 576 ARG 0.008 0.001 ARG A 512 =============================================================================== Job complete usr+sys time: 1270.84 seconds wall clock time: 23 minutes 41.26 seconds (1421.26 seconds total)