Starting phenix.real_space_refine on Thu Nov 14 06:01:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5x_41935/11_2024/8u5x_41935.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5x_41935/11_2024/8u5x_41935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5x_41935/11_2024/8u5x_41935.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5x_41935/11_2024/8u5x_41935.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5x_41935/11_2024/8u5x_41935.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u5x_41935/11_2024/8u5x_41935.cif" } resolution = 2.79 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.072 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 2984 2.51 5 N 688 2.21 5 O 753 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 4453 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4440 Classifications: {'peptide': 569} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 547} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'IAC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.21, per 1000 atoms: 0.72 Number of scatterers: 4453 At special positions: 0 Unit cell: (93.0804, 72.0265, 77.567, 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 753 8.00 N 688 7.00 C 2984 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: 1.16 Conformation dependent library (CDL) restraints added in 553.3 milliseconds 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1064 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 91.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 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: 3.961A pdb=" N LYS A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 4.007A 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 removed outlier: 3.622A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' 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 Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 166 through 196 removed outlier: 4.328A 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 251 removed outlier: 4.205A pdb=" N ASN A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 265 removed outlier: 3.561A 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: 4.308A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.609A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 439 through 474 removed outlier: 3.556A pdb=" N GLY A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 503 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 Processing helix chain 'A' and resid 655 through 683 removed outlier: 3.688A pdb=" N GLY A 668 " --> pdb=" O LEU A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 711 removed outlier: 5.726A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 706 " --> pdb=" O GLY A 702 " (cutoff:3.500A) 374 hydrogen bonds defined for protein. 1101 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: 1.43 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1306 1.34 - 1.46: 833 1.46 - 1.57: 2377 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 4561 Sorted by residual: bond pdb=" C1 IAC A 901 " pdb=" C7 IAC A 901 " ideal model delta sigma weight residual 1.433 1.364 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C IAC A 901 " pdb=" C1 IAC A 901 " ideal model delta sigma weight residual 1.414 1.366 0.048 2.00e-02 2.50e+03 5.71e+00 bond pdb=" C17 IAC A 901 " pdb=" C7 IAC A 901 " ideal model delta sigma weight residual 1.487 1.532 -0.045 2.00e-02 2.50e+03 4.95e+00 bond pdb=" CA TRP A 679 " pdb=" C TRP A 679 " ideal model delta sigma weight residual 1.524 1.497 0.028 1.28e-02 6.10e+03 4.73e+00 bond pdb=" CB VAL A 425 " pdb=" CG2 VAL A 425 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.63e+00 ... (remaining 4556 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 6082 2.70 - 5.40: 109 5.40 - 8.10: 9 8.10 - 10.80: 0 10.80 - 13.50: 2 Bond angle restraints: 6202 Sorted by residual: angle pdb=" C17 IAC A 901 " pdb=" C7 IAC A 901 " pdb=" C8 IAC A 901 " ideal model delta sigma weight residual 127.34 113.84 13.50 3.00e+00 1.11e-01 2.03e+01 angle pdb=" C1 IAC A 901 " pdb=" C7 IAC A 901 " pdb=" C17 IAC A 901 " ideal model delta sigma weight residual 126.92 138.72 -11.80 3.00e+00 1.11e-01 1.55e+01 angle pdb=" CA TRP A 679 " pdb=" CB TRP A 679 " pdb=" CG TRP A 679 " ideal model delta sigma weight residual 113.60 106.51 7.09 1.90e+00 2.77e-01 1.39e+01 angle pdb=" CA PHE A 221 " pdb=" CB PHE A 221 " pdb=" CG PHE A 221 " ideal model delta sigma weight residual 113.80 117.33 -3.53 1.00e+00 1.00e+00 1.25e+01 angle pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " pdb=" CG TYR A 451 " ideal model delta sigma weight residual 113.90 119.97 -6.07 1.80e+00 3.09e-01 1.14e+01 ... (remaining 6197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 2474 17.37 - 34.75: 155 34.75 - 52.12: 21 52.12 - 69.49: 8 69.49 - 86.86: 1 Dihedral angle restraints: 2659 sinusoidal: 1008 harmonic: 1651 Sorted by residual: dihedral pdb=" CA GLN A 654 " pdb=" C GLN A 654 " pdb=" N LEU A 655 " pdb=" CA LEU A 655 " ideal model delta harmonic sigma weight residual 180.00 -151.46 -28.54 0 5.00e+00 4.00e-02 3.26e+01 dihedral pdb=" CA TYR A 516 " pdb=" C TYR A 516 " pdb=" N GLY A 517 " pdb=" CA GLY A 517 " ideal model delta harmonic sigma weight residual 180.00 154.17 25.83 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA GLN A 409 " pdb=" C GLN A 409 " pdb=" N LEU A 410 " pdb=" CA LEU A 410 " ideal model delta harmonic sigma weight residual 180.00 158.19 21.81 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 2656 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 501 0.043 - 0.087: 189 0.087 - 0.130: 47 0.130 - 0.174: 7 0.174 - 0.217: 2 Chirality restraints: 746 Sorted by residual: 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 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CB THR A 457 " pdb=" CA THR A 457 " pdb=" OG1 THR A 457 " pdb=" CG2 THR A 457 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA ILE A 65 " pdb=" N ILE A 65 " pdb=" C ILE A 65 " pdb=" CB ILE A 65 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 743 not shown) Planarity restraints: 747 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 221 " -0.030 2.00e-02 2.50e+03 2.34e-02 9.59e+00 pdb=" CG PHE A 221 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 PHE A 221 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 221 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 221 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE A 221 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 221 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 708 " -0.030 2.00e-02 2.50e+03 2.10e-02 7.72e+00 pdb=" CG PHE A 708 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 708 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 708 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 708 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 708 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 708 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 320 " 0.036 2.00e-02 2.50e+03 1.88e-02 7.09e+00 pdb=" CG TYR A 320 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR A 320 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR A 320 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 320 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 320 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 320 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 320 " 0.014 2.00e-02 2.50e+03 ... (remaining 744 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 1959 2.92 - 3.42: 5094 3.42 - 3.91: 7920 3.91 - 4.41: 9447 4.41 - 4.90: 14808 Nonbonded interactions: 39228 Sorted by model distance: nonbonded pdb=" OH TYR A 359 " pdb=" OD2 ASP A 385 " model vdw 2.428 3.040 nonbonded pdb=" O ASN A 682 " pdb=" N GLU A 684 " model vdw 2.455 3.120 nonbonded pdb=" O VAL A 117 " pdb=" OG1 THR A 121 " model vdw 2.459 3.040 nonbonded pdb=" O VAL A 340 " pdb=" OG1 THR A 344 " model vdw 2.479 3.040 nonbonded pdb=" O ILE A 400 " pdb=" OG SER A 404 " model vdw 2.498 3.040 ... (remaining 39223 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: 0.050 Process input model: 14.840 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 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 4561 Z= 0.509 Angle : 0.875 13.500 6202 Z= 0.471 Chirality : 0.048 0.217 746 Planarity : 0.007 0.055 747 Dihedral : 12.003 86.862 1595 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.61 % Allowed : 2.86 % Favored : 96.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.95 (0.31), residues: 565 helix: -0.48 (0.21), residues: 452 sheet: None (None), residues: 0 loop : -0.50 (0.56), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.004 TRP A 679 HIS 0.008 0.004 HIS A 310 PHE 0.053 0.004 PHE A 221 TYR 0.036 0.004 TYR A 320 ARG 0.003 0.001 ARG A 41 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 136 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8207 (tt0) cc_final: 0.6527 (tp30) REVERT: A 71 LYS cc_start: 0.7846 (mtpt) cc_final: 0.7047 (pptt) REVERT: A 216 GLN cc_start: 0.8219 (mt0) cc_final: 0.7952 (mt0) REVERT: A 347 MET cc_start: 0.8699 (tmm) cc_final: 0.8462 (tmm) REVERT: A 359 TYR cc_start: 0.8855 (t80) cc_final: 0.8083 (t80) outliers start: 3 outliers final: 2 residues processed: 138 average time/residue: 0.9683 time to fit residues: 139.6788 Evaluate side-chains 99 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 447 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 26 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN A 202 ASN A 412 HIS A 658 HIS A 672 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4561 Z= 0.268 Angle : 0.732 8.423 6202 Z= 0.367 Chirality : 0.044 0.189 746 Planarity : 0.005 0.040 747 Dihedral : 5.721 46.244 604 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.06 % Allowed : 13.67 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.34), residues: 565 helix: 1.28 (0.23), residues: 460 sheet: None (None), residues: 0 loop : -0.04 (0.59), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 432 HIS 0.006 0.002 HIS A 658 PHE 0.032 0.002 PHE A 221 TYR 0.013 0.002 TYR A 516 ARG 0.004 0.001 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8161 (tt0) cc_final: 0.6188 (tp30) REVERT: A 71 LYS cc_start: 0.7786 (mtpt) cc_final: 0.7487 (mmmt) REVERT: A 299 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8392 (mt-10) REVERT: A 347 MET cc_start: 0.8631 (tmm) cc_final: 0.8408 (tmm) REVERT: A 451 TYR cc_start: 0.6735 (m-10) cc_final: 0.6080 (m-10) REVERT: A 492 PRO cc_start: 0.8348 (Cg_exo) cc_final: 0.8131 (Cg_endo) outliers start: 15 outliers final: 4 residues processed: 118 average time/residue: 0.9058 time to fit residues: 112.2079 Evaluate side-chains 102 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 662 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 50 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 433 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 4561 Z= 0.244 Angle : 0.711 10.971 6202 Z= 0.353 Chirality : 0.043 0.165 746 Planarity : 0.005 0.038 747 Dihedral : 5.047 39.287 602 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.27 % Allowed : 17.35 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.93 (0.35), residues: 565 helix: 1.63 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -0.05 (0.60), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 489 HIS 0.002 0.001 HIS A 505 PHE 0.030 0.002 PHE A 221 TYR 0.010 0.002 TYR A 451 ARG 0.005 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 102 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7571 (mtm-85) REVERT: A 71 LYS cc_start: 0.7779 (mtpt) cc_final: 0.7425 (mmmt) REVERT: A 130 ARG cc_start: 0.8210 (ptp90) cc_final: 0.7842 (ptp90) REVERT: A 193 TRP cc_start: 0.8161 (t60) cc_final: 0.7874 (t60) REVERT: A 203 LYS cc_start: 0.7834 (mmpt) cc_final: 0.7599 (mtmm) REVERT: A 347 MET cc_start: 0.8662 (tmm) cc_final: 0.8448 (tmm) REVERT: A 447 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7866 (p90) REVERT: A 459 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8197 (mt) outliers start: 16 outliers final: 3 residues processed: 109 average time/residue: 1.0165 time to fit residues: 115.6977 Evaluate side-chains 95 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 447 PHE Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 654 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4561 Z= 0.206 Angle : 0.679 8.347 6202 Z= 0.337 Chirality : 0.042 0.158 746 Planarity : 0.005 0.037 747 Dihedral : 4.806 34.649 602 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.65 % Allowed : 18.57 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 565 helix: 1.71 (0.24), residues: 460 sheet: None (None), residues: 0 loop : -0.15 (0.62), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 679 HIS 0.001 0.000 HIS A 505 PHE 0.028 0.002 PHE A 221 TYR 0.023 0.002 TYR A 689 ARG 0.006 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7568 (mtm-85) REVERT: A 71 LYS cc_start: 0.7737 (mtpt) cc_final: 0.7404 (mmmt) REVERT: A 104 TYR cc_start: 0.8107 (m-80) cc_final: 0.7898 (m-80) REVERT: A 130 ARG cc_start: 0.8233 (ptp90) cc_final: 0.7866 (ptp90) REVERT: A 193 TRP cc_start: 0.8115 (t60) cc_final: 0.7890 (t60) REVERT: A 234 ASP cc_start: 0.8715 (t0) cc_final: 0.8380 (t0) REVERT: A 299 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8270 (mt-10) REVERT: A 347 MET cc_start: 0.8654 (tmm) cc_final: 0.8453 (tmm) REVERT: A 409 GLN cc_start: 0.5578 (OUTLIER) cc_final: 0.5330 (tm-30) REVERT: A 459 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8165 (mt) outliers start: 13 outliers final: 5 residues processed: 118 average time/residue: 1.0459 time to fit residues: 128.6440 Evaluate side-chains 100 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 457 THR Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 37 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- 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: 0.8124 moved from start: 0.4333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4561 Z= 0.236 Angle : 0.713 14.364 6202 Z= 0.349 Chirality : 0.043 0.174 746 Planarity : 0.005 0.037 747 Dihedral : 4.484 20.059 600 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.65 % Allowed : 21.84 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.12 (0.35), residues: 565 helix: 1.78 (0.24), residues: 459 sheet: None (None), residues: 0 loop : -0.12 (0.61), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 432 HIS 0.001 0.001 HIS A 658 PHE 0.029 0.002 PHE A 221 TYR 0.014 0.002 TYR A 451 ARG 0.006 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7565 (mtm-85) REVERT: A 61 ARG cc_start: 0.8650 (mmm-85) cc_final: 0.8442 (mmm-85) REVERT: A 71 LYS cc_start: 0.7560 (mtpt) cc_final: 0.7279 (mmmt) REVERT: A 130 ARG cc_start: 0.8231 (ptp90) cc_final: 0.7853 (ptp90) REVERT: A 203 LYS cc_start: 0.7724 (mmpt) cc_final: 0.7444 (mtmm) REVERT: A 299 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8320 (mt-10) REVERT: A 409 GLN cc_start: 0.5856 (OUTLIER) cc_final: 0.5189 (tm-30) REVERT: A 459 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8126 (mt) outliers start: 13 outliers final: 4 residues processed: 111 average time/residue: 0.9247 time to fit residues: 107.4131 Evaluate side-chains 99 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 459 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 4561 Z= 0.210 Angle : 0.698 12.145 6202 Z= 0.340 Chirality : 0.043 0.183 746 Planarity : 0.004 0.039 747 Dihedral : 4.381 19.443 600 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.65 % Allowed : 21.22 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.34 (0.36), residues: 565 helix: 1.88 (0.24), residues: 460 sheet: None (None), residues: 0 loop : 0.24 (0.65), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 679 HIS 0.003 0.001 HIS A 505 PHE 0.027 0.002 PHE A 221 TYR 0.017 0.002 TYR A 451 ARG 0.005 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7615 (mtpt) cc_final: 0.7284 (mmmt) REVERT: A 130 ARG cc_start: 0.8242 (ptp90) cc_final: 0.7885 (ptp90) REVERT: A 203 LYS cc_start: 0.7694 (mmpt) cc_final: 0.7488 (mtmm) REVERT: A 234 ASP cc_start: 0.8707 (t0) cc_final: 0.8390 (t0) REVERT: A 295 ARG cc_start: 0.8571 (ttp80) cc_final: 0.8231 (mtm110) REVERT: A 299 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8295 (mt-10) REVERT: A 430 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7680 (mmm) REVERT: A 459 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8240 (mt) REVERT: A 516 TYR cc_start: 0.7353 (m-80) cc_final: 0.6964 (t80) outliers start: 13 outliers final: 2 residues processed: 107 average time/residue: 0.9422 time to fit residues: 105.6964 Evaluate side-chains 90 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 86 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 471 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.0070 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4561 Z= 0.213 Angle : 0.736 13.423 6202 Z= 0.351 Chirality : 0.045 0.221 746 Planarity : 0.005 0.040 747 Dihedral : 4.370 20.058 600 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.04 % Allowed : 24.49 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.33 (0.36), residues: 565 helix: 1.84 (0.24), residues: 463 sheet: None (None), residues: 0 loop : 0.39 (0.69), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 679 HIS 0.003 0.001 HIS A 505 PHE 0.028 0.002 PHE A 221 TYR 0.019 0.002 TYR A 451 ARG 0.007 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 99 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7620 (mtpt) cc_final: 0.7285 (mmmt) REVERT: A 130 ARG cc_start: 0.8256 (ptp90) cc_final: 0.7896 (ptp90) REVERT: A 295 ARG cc_start: 0.8559 (ttp80) cc_final: 0.8238 (mtm110) REVERT: A 299 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8316 (mt-10) REVERT: A 430 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7686 (mmm) REVERT: A 459 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8256 (mp) REVERT: A 516 TYR cc_start: 0.7319 (m-80) cc_final: 0.6805 (t80) REVERT: A 542 MET cc_start: 0.7467 (tmm) cc_final: 0.7263 (tmm) outliers start: 10 outliers final: 3 residues processed: 101 average time/residue: 0.9542 time to fit residues: 100.8224 Evaluate side-chains 100 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 95 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 532 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4561 Z= 0.253 Angle : 0.719 11.289 6202 Z= 0.354 Chirality : 0.046 0.269 746 Planarity : 0.005 0.041 747 Dihedral : 4.362 19.011 600 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.24 % Allowed : 24.29 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.36), residues: 565 helix: 1.86 (0.24), residues: 460 sheet: None (None), residues: 0 loop : 0.22 (0.67), residues: 105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 679 HIS 0.003 0.001 HIS A 505 PHE 0.029 0.002 PHE A 221 TYR 0.021 0.002 TYR A 104 ARG 0.006 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7600 (mtpt) cc_final: 0.7256 (mmmt) REVERT: A 130 ARG cc_start: 0.8327 (ptp90) cc_final: 0.7958 (ptp90) REVERT: A 203 LYS cc_start: 0.7743 (mmpt) cc_final: 0.7374 (mtmm) REVERT: A 234 ASP cc_start: 0.8723 (t0) cc_final: 0.8418 (t0) REVERT: A 295 ARG cc_start: 0.8578 (ttp80) cc_final: 0.8234 (mtm110) REVERT: A 430 MET cc_start: 0.8440 (OUTLIER) cc_final: 0.7487 (mtm) REVERT: A 459 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8266 (mp) REVERT: A 516 TYR cc_start: 0.7327 (m-80) cc_final: 0.7118 (t80) REVERT: A 542 MET cc_start: 0.7561 (tmm) cc_final: 0.7314 (tmm) outliers start: 11 outliers final: 5 residues processed: 101 average time/residue: 0.9575 time to fit residues: 101.5701 Evaluate side-chains 87 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 511 ASP Chi-restraints excluded: chain A residue 532 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.0470 chunk 47 optimal weight: 0.0000 chunk 50 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 overall best weight: 0.4882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN A 700 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4561 Z= 0.205 Angle : 0.743 11.375 6202 Z= 0.362 Chirality : 0.047 0.283 746 Planarity : 0.005 0.041 747 Dihedral : 4.359 17.255 600 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.63 % Allowed : 24.49 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.28 (0.36), residues: 565 helix: 1.81 (0.24), residues: 463 sheet: None (None), residues: 0 loop : 0.28 (0.68), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 679 HIS 0.002 0.001 HIS A 505 PHE 0.026 0.002 PHE A 221 TYR 0.017 0.002 TYR A 689 ARG 0.007 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7594 (mtpt) cc_final: 0.7260 (mmmt) REVERT: A 130 ARG cc_start: 0.8266 (ptp90) cc_final: 0.7879 (ptp90) REVERT: A 203 LYS cc_start: 0.7665 (mmpt) cc_final: 0.7375 (mtmm) REVERT: A 430 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7667 (mmm) REVERT: A 459 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8294 (mp) REVERT: A 521 MET cc_start: 0.6435 (mmt) cc_final: 0.6135 (mmt) REVERT: A 542 MET cc_start: 0.7501 (tmm) cc_final: 0.7283 (tmm) outliers start: 8 outliers final: 2 residues processed: 95 average time/residue: 1.0487 time to fit residues: 104.3056 Evaluate side-chains 88 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 84 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 532 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 4561 Z= 0.242 Angle : 0.800 11.384 6202 Z= 0.390 Chirality : 0.048 0.301 746 Planarity : 0.005 0.041 747 Dihedral : 4.423 18.574 600 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.02 % Allowed : 26.12 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.08 (0.36), residues: 565 helix: 1.74 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -0.14 (0.67), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 396 HIS 0.003 0.001 HIS A 505 PHE 0.028 0.002 PHE A 221 TYR 0.021 0.002 TYR A 689 ARG 0.007 0.001 ARG A 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: A 71 LYS cc_start: 0.7653 (mtpt) cc_final: 0.7249 (mmmt) REVERT: A 130 ARG cc_start: 0.8267 (ptp90) cc_final: 0.7895 (ptp90) REVERT: A 203 LYS cc_start: 0.7565 (mmpt) cc_final: 0.7263 (mtmm) REVERT: A 295 ARG cc_start: 0.8528 (ttp80) cc_final: 0.8235 (mtm110) REVERT: A 430 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7595 (mmm) REVERT: A 459 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8320 (mp) REVERT: A 542 MET cc_start: 0.7535 (tmm) cc_final: 0.7230 (tpt) outliers start: 5 outliers final: 3 residues processed: 82 average time/residue: 1.0844 time to fit residues: 93.1728 Evaluate side-chains 78 residues out of total 495 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain A residue 418 LEU Chi-restraints excluded: chain A residue 430 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 532 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 181 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.137937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.106365 restraints weight = 8160.825| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.70 r_work: 0.3427 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.5443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 4561 Z= 0.243 Angle : 0.823 11.733 6202 Z= 0.402 Chirality : 0.050 0.288 746 Planarity : 0.005 0.041 747 Dihedral : 4.467 18.585 600 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.63 % Allowed : 26.94 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 2.01 (0.36), residues: 565 helix: 1.71 (0.24), residues: 463 sheet: None (None), residues: 0 loop : -0.26 (0.65), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 679 HIS 0.002 0.001 HIS A 505 PHE 0.028 0.002 PHE A 221 TYR 0.022 0.002 TYR A 689 ARG 0.007 0.001 ARG A 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2079.94 seconds wall clock time: 38 minutes 3.08 seconds (2283.08 seconds total)