Starting phenix.real_space_refine on Thu Nov 14 05:47:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5v_41934/11_2024/8u5v_41934.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5v_41934/11_2024/8u5v_41934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5v_41934/11_2024/8u5v_41934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5v_41934/11_2024/8u5v_41934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5v_41934/11_2024/8u5v_41934.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5v_41934/11_2024/8u5v_41934.cif" } resolution = 2.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.075 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 2957 2.51 5 N 674 2.21 5 O 738 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-5513/modules/chem_data/mon_lib" Total number of atoms: 4397 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 556, 4359 Classifications: {'peptide': 556} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 535} Chain breaks: 4 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {'IAC': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'Y01:plan-2': 1, 'Y01:plan-1': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 2.88, per 1000 atoms: 0.65 Number of scatterers: 4397 At special positions: 0 Unit cell: (90.8642, 69.8103, 76.4589, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 738 8.00 N 674 7.00 C 2957 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: 1.36 Conformation dependent library (CDL) restraints added in 551.0 milliseconds 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1042 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 90.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 66 through 80 removed outlier: 3.719A pdb=" N LYS A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 94 through 98 Processing helix chain 'A' and resid 99 through 125 Processing helix chain 'A' and resid 129 through 143 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.539A pdb=" N ILE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 196 removed outlier: 3.800A pdb=" N TYR A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ILE A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Proline residue: A 174 - end of helix Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 202 through 216 Processing helix chain 'A' and resid 217 through 234 Processing helix chain 'A' and resid 238 through 265 removed outlier: 4.252A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLY A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 326 through 337 removed outlier: 4.280A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 367 Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 411 through 436 removed outlier: 3.671A pdb=" N PHE A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 474 Processing helix chain 'A' and resid 480 through 500 Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 516 through 544 removed outlier: 3.564A pdb=" N GLN A 544 " --> pdb=" O MET A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 679 Processing helix chain 'A' and resid 688 through 711 removed outlier: 5.763A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) 368 hydrogen bonds defined for protein. 1086 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.26 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 649 1.30 - 1.43: 1202 1.43 - 1.55: 2607 1.55 - 1.68: 1 1.68 - 1.81: 45 Bond restraints: 4504 Sorted by residual: bond pdb=" C PHE A 447 " pdb=" O PHE A 447 " ideal model delta sigma weight residual 1.237 1.168 0.069 1.19e-02 7.06e+03 3.35e+01 bond pdb=" C TYR A 689 " pdb=" O TYR A 689 " ideal model delta sigma weight residual 1.237 1.191 0.045 1.17e-02 7.31e+03 1.49e+01 bond pdb=" C1 IAC A 901 " pdb=" C7 IAC A 901 " ideal model delta sigma weight residual 1.433 1.366 0.067 2.00e-02 2.50e+03 1.13e+01 bond pdb=" C LEU A 692 " pdb=" O LEU A 692 " ideal model delta sigma weight residual 1.236 1.196 0.040 1.31e-02 5.83e+03 9.41e+00 bond pdb=" N VAL A 448 " pdb=" CA VAL A 448 " ideal model delta sigma weight residual 1.462 1.496 -0.034 1.18e-02 7.18e+03 8.32e+00 ... (remaining 4499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 5860 2.35 - 4.70: 232 4.70 - 7.05: 25 7.05 - 9.40: 6 9.40 - 11.75: 2 Bond angle restraints: 6125 Sorted by residual: angle pdb=" N THR A 457 " pdb=" CA THR A 457 " pdb=" C THR A 457 " ideal model delta sigma weight residual 111.36 103.41 7.95 1.09e+00 8.42e-01 5.32e+01 angle pdb=" N GLN A 693 " pdb=" CA GLN A 693 " pdb=" C GLN A 693 " ideal model delta sigma weight residual 111.36 103.46 7.90 1.09e+00 8.42e-01 5.26e+01 angle pdb=" CA TYR A 689 " pdb=" C TYR A 689 " pdb=" O TYR A 689 " ideal model delta sigma weight residual 120.55 114.61 5.94 1.06e+00 8.90e-01 3.14e+01 angle pdb=" C TYR A 451 " pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " ideal model delta sigma weight residual 110.85 119.85 -9.00 1.70e+00 3.46e-01 2.80e+01 angle pdb=" C TRP A 460 " pdb=" N THR A 461 " pdb=" CA THR A 461 " ideal model delta sigma weight residual 120.28 114.12 6.16 1.34e+00 5.57e-01 2.12e+01 ... (remaining 6120 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 14.79: 2423 14.79 - 29.57: 200 29.57 - 44.35: 30 44.35 - 59.13: 13 59.13 - 73.91: 3 Dihedral angle restraints: 2669 sinusoidal: 1056 harmonic: 1613 Sorted by residual: dihedral pdb=" C TYR A 451 " pdb=" N TYR A 451 " pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " ideal model delta harmonic sigma weight residual -122.60 -139.64 17.04 0 2.50e+00 1.60e-01 4.65e+01 dihedral pdb=" N TYR A 451 " pdb=" C TYR A 451 " pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " ideal model delta harmonic sigma weight residual 122.80 136.98 -14.18 0 2.50e+00 1.60e-01 3.22e+01 dihedral pdb=" CA THR A 196 " pdb=" C THR A 196 " pdb=" N GLN A 197 " pdb=" CA GLN A 197 " ideal model delta harmonic sigma weight residual -180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 2666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 705 0.118 - 0.237: 34 0.237 - 0.355: 0 0.355 - 0.473: 0 0.473 - 0.592: 1 Chirality restraints: 740 Sorted by residual: chirality pdb=" CA TYR A 451 " pdb=" N TYR A 451 " pdb=" C TYR A 451 " pdb=" CB TYR A 451 " both_signs ideal model delta sigma weight residual False 2.51 1.92 0.59 2.00e-01 2.50e+01 8.75e+00 chirality pdb=" CA PHE A 221 " pdb=" N PHE A 221 " pdb=" C PHE A 221 " pdb=" CB PHE A 221 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA PHE A 695 " pdb=" N PHE A 695 " pdb=" C PHE A 695 " pdb=" CB PHE A 695 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 737 not shown) Planarity restraints: 729 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 320 " 0.087 2.00e-02 2.50e+03 4.45e-02 3.95e+01 pdb=" CG TYR A 320 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR A 320 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR A 320 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 TYR A 320 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 320 " -0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 320 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR A 320 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 221 " -0.038 2.00e-02 2.50e+03 2.78e-02 1.35e+01 pdb=" CG PHE A 221 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE A 221 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 221 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 221 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE A 221 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 221 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 457 " 0.017 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C THR A 457 " -0.061 2.00e-02 2.50e+03 pdb=" O THR A 457 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR A 458 " 0.021 2.00e-02 2.50e+03 ... (remaining 726 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 1866 2.92 - 3.42: 4944 3.42 - 3.91: 7927 3.91 - 4.41: 9244 4.41 - 4.90: 14735 Nonbonded interactions: 38716 Sorted by model distance: nonbonded pdb=" O TYR A 458 " pdb=" OG SER A 531 " model vdw 2.429 3.040 nonbonded pdb=" OH TYR A 359 " pdb=" OD2 ASP A 385 " model vdw 2.458 3.040 nonbonded pdb=" O VAL A 117 " pdb=" OG1 THR A 121 " model vdw 2.510 3.040 nonbonded pdb=" O VAL A 340 " pdb=" OG1 THR A 344 " model vdw 2.544 3.040 nonbonded pdb=" OD1 ASP A 99 " pdb=" OG SER A 101 " model vdw 2.547 3.040 ... (remaining 38711 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: 0.120 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.420 Find NCS groups from input model: 0.040 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:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 : 0.008 0.069 4504 Z= 0.514 Angle : 1.069 11.747 6125 Z= 0.649 Chirality : 0.059 0.592 740 Planarity : 0.008 0.047 729 Dihedral : 11.857 73.905 1627 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.24 % Allowed : 2.89 % Favored : 95.87 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.32), residues: 546 helix: 0.07 (0.22), residues: 452 sheet: None (None), residues: 0 loop : -0.51 (0.63), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.007 TRP A 489 HIS 0.005 0.002 HIS A 658 PHE 0.061 0.006 PHE A 221 TYR 0.087 0.008 TYR A 320 ARG 0.005 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.7874 (mt0) cc_final: 0.7543 (mt0) REVERT: A 71 LYS cc_start: 0.7667 (mtpt) cc_final: 0.7208 (pptt) REVERT: A 76 PHE cc_start: 0.8903 (t80) cc_final: 0.8682 (t80) REVERT: A 159 GLN cc_start: 0.8590 (tt0) cc_final: 0.8179 (pt0) REVERT: A 193 TRP cc_start: 0.7977 (t60) cc_final: 0.7738 (t60) REVERT: A 212 LEU cc_start: 0.8971 (tp) cc_final: 0.8707 (tp) REVERT: A 234 ASP cc_start: 0.8428 (t0) cc_final: 0.8220 (t0) REVERT: A 347 MET cc_start: 0.9092 (tmm) cc_final: 0.8809 (tmm) REVERT: A 434 PHE cc_start: 0.7769 (m-80) cc_final: 0.7487 (m-80) REVERT: A 469 PHE cc_start: 0.8024 (t80) cc_final: 0.7770 (t80) outliers start: 6 outliers final: 2 residues processed: 157 average time/residue: 0.9478 time to fit residues: 155.6028 Evaluate side-chains 102 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 100 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 511 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 46 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 4504 Z= 0.337 Angle : 0.730 7.360 6125 Z= 0.371 Chirality : 0.045 0.171 740 Planarity : 0.005 0.032 729 Dihedral : 7.261 109.085 651 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.51 % Allowed : 13.84 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.35), residues: 546 helix: 1.61 (0.23), residues: 453 sheet: None (None), residues: 0 loop : 0.26 (0.68), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 396 HIS 0.003 0.001 HIS A 658 PHE 0.032 0.002 PHE A 221 TYR 0.027 0.003 TYR A 689 ARG 0.003 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 PHE cc_start: 0.8922 (t80) cc_final: 0.8659 (t80) REVERT: A 212 LEU cc_start: 0.8986 (tp) cc_final: 0.8736 (tp) REVERT: A 385 ASP cc_start: 0.8292 (m-30) cc_final: 0.8082 (m-30) REVERT: A 469 PHE cc_start: 0.8173 (t80) cc_final: 0.7922 (t80) outliers start: 17 outliers final: 4 residues processed: 120 average time/residue: 0.9903 time to fit residues: 123.9620 Evaluate side-chains 97 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 93 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 676 CYS Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 50 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 40.0000 chunk 49 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 ASN A 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4504 Z= 0.211 Angle : 0.691 10.716 6125 Z= 0.334 Chirality : 0.043 0.166 740 Planarity : 0.004 0.035 729 Dihedral : 5.535 57.369 649 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.31 % Allowed : 16.94 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.35), residues: 546 helix: 1.93 (0.23), residues: 452 sheet: None (None), residues: 0 loop : 0.43 (0.73), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 193 HIS 0.001 0.000 HIS A 412 PHE 0.029 0.002 PHE A 221 TYR 0.024 0.002 TYR A 451 ARG 0.002 0.000 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7825 (mtm180) REVERT: A 76 PHE cc_start: 0.8858 (t80) cc_final: 0.8601 (t80) REVERT: A 212 LEU cc_start: 0.8918 (tp) cc_final: 0.8713 (tp) REVERT: A 235 ARG cc_start: 0.8717 (mtm-85) cc_final: 0.8407 (mtm-85) REVERT: A 295 ARG cc_start: 0.8582 (ttp80) cc_final: 0.7951 (ttt-90) REVERT: A 299 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: A 466 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8203 (mt) REVERT: A 469 PHE cc_start: 0.8275 (t80) cc_final: 0.8000 (t80) REVERT: A 692 LEU cc_start: 0.8594 (tp) cc_final: 0.8382 (tp) outliers start: 16 outliers final: 4 residues processed: 119 average time/residue: 0.9626 time to fit residues: 120.2043 Evaluate side-chains 103 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 97 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 49 optimal weight: 5.9990 chunk 37 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 33 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 47 optimal weight: 0.0980 chunk 14 optimal weight: 5.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4504 Z= 0.271 Angle : 0.744 14.026 6125 Z= 0.348 Chirality : 0.044 0.231 740 Planarity : 0.004 0.035 729 Dihedral : 5.421 54.048 649 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.69 % Allowed : 19.42 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.35), residues: 546 helix: 1.90 (0.23), residues: 457 sheet: None (None), residues: 0 loop : -0.29 (0.71), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 193 HIS 0.001 0.001 HIS A 658 PHE 0.029 0.002 PHE A 221 TYR 0.022 0.002 TYR A 451 ARG 0.002 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 100 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 164 GLU cc_start: 0.8783 (pm20) cc_final: 0.8578 (pm20) REVERT: A 235 ARG cc_start: 0.8699 (mtm-85) cc_final: 0.8420 (mtm-85) REVERT: A 295 ARG cc_start: 0.8593 (ttp80) cc_final: 0.8291 (ttp80) REVERT: A 299 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: A 466 ILE cc_start: 0.8379 (OUTLIER) cc_final: 0.8142 (mt) REVERT: A 469 PHE cc_start: 0.8271 (t80) cc_final: 0.8000 (t80) outliers start: 13 outliers final: 6 residues processed: 108 average time/residue: 0.9742 time to fit residues: 110.0093 Evaluate side-chains 98 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 44 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 45 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 27 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 4504 Z= 0.286 Angle : 0.744 11.755 6125 Z= 0.348 Chirality : 0.048 0.370 740 Planarity : 0.004 0.034 729 Dihedral : 5.375 53.873 649 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 3.51 % Allowed : 20.66 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.36), residues: 546 helix: 1.92 (0.23), residues: 457 sheet: None (None), residues: 0 loop : -0.14 (0.74), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 193 HIS 0.001 0.001 HIS A 412 PHE 0.029 0.002 PHE A 221 TYR 0.023 0.002 TYR A 689 ARG 0.002 0.000 ARG A 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8670 (mtm-85) cc_final: 0.8385 (mtm-85) REVERT: A 242 GLU cc_start: 0.7924 (tt0) cc_final: 0.7691 (tt0) REVERT: A 299 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: A 469 PHE cc_start: 0.8265 (t80) cc_final: 0.7970 (t80) outliers start: 17 outliers final: 8 residues processed: 102 average time/residue: 0.8751 time to fit residues: 93.8788 Evaluate side-chains 98 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.0980 chunk 13 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4504 Z= 0.205 Angle : 0.722 10.265 6125 Z= 0.339 Chirality : 0.045 0.347 740 Planarity : 0.004 0.034 729 Dihedral : 5.044 56.275 647 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 3.10 % Allowed : 21.90 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.51 (0.36), residues: 546 helix: 2.02 (0.23), residues: 457 sheet: None (None), residues: 0 loop : -0.13 (0.74), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 193 HIS 0.002 0.001 HIS A 658 PHE 0.027 0.002 PHE A 221 TYR 0.025 0.002 TYR A 104 ARG 0.004 0.001 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.7871 (m-80) cc_final: 0.7559 (m-80) REVERT: A 146 ASP cc_start: 0.8867 (m-30) cc_final: 0.8602 (m-30) REVERT: A 242 GLU cc_start: 0.7864 (tt0) cc_final: 0.7371 (tt0) REVERT: A 246 ASP cc_start: 0.8367 (m-30) cc_final: 0.8058 (m-30) REVERT: A 299 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7709 (mp0) REVERT: A 469 PHE cc_start: 0.8209 (t80) cc_final: 0.7935 (t80) outliers start: 15 outliers final: 10 residues processed: 121 average time/residue: 0.9267 time to fit residues: 117.4407 Evaluate side-chains 97 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 5 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 0.0270 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4504 Z= 0.209 Angle : 0.745 9.984 6125 Z= 0.351 Chirality : 0.046 0.367 740 Planarity : 0.004 0.038 729 Dihedral : 5.000 54.455 647 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.10 % Allowed : 24.17 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.36), residues: 546 helix: 2.11 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -0.08 (0.77), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 460 HIS 0.002 0.001 HIS A 412 PHE 0.027 0.002 PHE A 221 TYR 0.027 0.002 TYR A 451 ARG 0.007 0.001 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8240 (mtm180) cc_final: 0.7958 (mtp180) REVERT: A 242 GLU cc_start: 0.7834 (tt0) cc_final: 0.7616 (tt0) REVERT: A 299 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: A 469 PHE cc_start: 0.8177 (t80) cc_final: 0.7892 (t80) outliers start: 15 outliers final: 11 residues processed: 105 average time/residue: 0.9332 time to fit residues: 102.7582 Evaluate side-chains 99 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 15 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 0.0270 chunk 36 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 50 optimal weight: 20.0000 chunk 46 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 overall best weight: 1.7242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4504 Z= 0.253 Angle : 0.774 13.240 6125 Z= 0.361 Chirality : 0.047 0.323 740 Planarity : 0.004 0.040 729 Dihedral : 5.028 53.752 647 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.51 % Allowed : 23.14 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.52 (0.36), residues: 546 helix: 2.01 (0.24), residues: 457 sheet: None (None), residues: 0 loop : -0.01 (0.77), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 460 HIS 0.003 0.001 HIS A 412 PHE 0.028 0.002 PHE A 221 TYR 0.030 0.002 TYR A 451 ARG 0.004 0.001 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8292 (mtm180) cc_final: 0.8054 (mtp180) REVERT: A 146 ASP cc_start: 0.8866 (m-30) cc_final: 0.8652 (m-30) REVERT: A 242 GLU cc_start: 0.7874 (tt0) cc_final: 0.7385 (tt0) REVERT: A 246 ASP cc_start: 0.8348 (m-30) cc_final: 0.8060 (m-30) REVERT: A 299 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: A 469 PHE cc_start: 0.8189 (t80) cc_final: 0.7908 (t80) REVERT: A 534 ILE cc_start: 0.8940 (mt) cc_final: 0.8644 (mm) outliers start: 17 outliers final: 12 residues processed: 113 average time/residue: 0.8681 time to fit residues: 103.2642 Evaluate side-chains 102 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 50 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4504 Z= 0.299 Angle : 0.828 14.268 6125 Z= 0.382 Chirality : 0.048 0.381 740 Planarity : 0.005 0.041 729 Dihedral : 5.079 52.785 647 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.89 % Allowed : 24.38 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.36), residues: 546 helix: 1.93 (0.24), residues: 458 sheet: None (None), residues: 0 loop : 0.05 (0.77), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 460 HIS 0.003 0.001 HIS A 658 PHE 0.029 0.002 PHE A 221 TYR 0.032 0.002 TYR A 104 ARG 0.005 0.001 ARG A 235 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 104 TYR cc_start: 0.7883 (m-80) cc_final: 0.7638 (m-80) REVERT: A 203 LYS cc_start: 0.8182 (mppt) cc_final: 0.7274 (mmmt) REVERT: A 299 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7786 (mp0) REVERT: A 469 PHE cc_start: 0.8218 (t80) cc_final: 0.7948 (t80) outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 0.8737 time to fit residues: 93.5794 Evaluate side-chains 99 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 272 LYS Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 24 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 50 optimal weight: 20.0000 chunk 43 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.0870 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 658 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4504 Z= 0.228 Angle : 0.816 13.128 6125 Z= 0.377 Chirality : 0.047 0.362 740 Planarity : 0.004 0.041 729 Dihedral : 5.038 55.076 647 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.69 % Allowed : 24.79 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.36), residues: 546 helix: 1.94 (0.24), residues: 457 sheet: None (None), residues: 0 loop : 0.13 (0.77), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 460 HIS 0.002 0.001 HIS A 658 PHE 0.026 0.002 PHE A 221 TYR 0.030 0.002 TYR A 104 ARG 0.007 0.001 ARG A 235 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1092 Ramachandran restraints generated. 546 Oldfield, 0 Emsley, 546 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8292 (mtm180) cc_final: 0.8021 (mtp180) REVERT: A 146 ASP cc_start: 0.8846 (m-30) cc_final: 0.8641 (m-30) REVERT: A 242 GLU cc_start: 0.7752 (tt0) cc_final: 0.7540 (tt0) REVERT: A 246 ASP cc_start: 0.8345 (m-30) cc_final: 0.8007 (m-30) REVERT: A 299 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: A 469 PHE cc_start: 0.8191 (t80) cc_final: 0.7920 (t80) outliers start: 13 outliers final: 10 residues processed: 108 average time/residue: 0.8184 time to fit residues: 93.1251 Evaluate side-chains 99 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 340 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 542 MET Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 696 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 55 random chunks: chunk 40 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 43 optimal weight: 7.9990 chunk 18 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.0570 chunk 38 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.127171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.097393 restraints weight = 7808.408| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.35 r_work: 0.3186 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4504 Z= 0.239 Angle : 0.813 14.939 6125 Z= 0.375 Chirality : 0.046 0.347 740 Planarity : 0.005 0.041 729 Dihedral : 5.018 54.114 647 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.69 % Allowed : 25.00 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.36), residues: 546 helix: 1.88 (0.24), residues: 457 sheet: None (None), residues: 0 loop : 0.22 (0.78), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 460 HIS 0.003 0.001 HIS A 658 PHE 0.026 0.002 PHE A 221 TYR 0.026 0.002 TYR A 451 ARG 0.007 0.001 ARG A 235 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2097.93 seconds wall clock time: 38 minutes 24.75 seconds (2304.75 seconds total)