Starting phenix.real_space_refine on Wed Mar 5 18:05:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cwo_30485/03_2025/7cwo_30485.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cwo_30485/03_2025/7cwo_30485.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cwo_30485/03_2025/7cwo_30485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cwo_30485/03_2025/7cwo_30485.map" model { file = "/net/cci-nas-00/data/ceres_data/7cwo_30485/03_2025/7cwo_30485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cwo_30485/03_2025/7cwo_30485.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 14 5.16 5 C 2063 2.51 5 N 558 2.21 5 O 619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3254 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1519 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 182} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 17 Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 117} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 101} Time building chain proxies: 2.61, per 1000 atoms: 0.80 Number of scatterers: 3254 At special positions: 0 Unit cell: (84.24, 70.72, 84.24, 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 14 16.00 O 619 8.00 N 558 7.00 C 2063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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: 0.77 Conformation dependent library (CDL) restraints added in 423.2 milliseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 7 sheets defined 10.7% alpha, 27.5% 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 337 through 342 Processing helix chain 'A' and resid 364 through 372 removed outlier: 4.140A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 389 removed outlier: 3.910A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 385 through 389' Processing helix chain 'A' and resid 405 through 409 removed outlier: 3.952A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.675A pdb=" N GLN A 506 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 removed outlier: 4.009A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.550A pdb=" N THR H 113 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 4 through 7 removed outlier: 11.870A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 10.398A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 11.550A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.278A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.345A pdb=" N GLN L 27 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ASP L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.606A pdb=" N GLU L 105 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 85 hydrogen bonds defined for protein. 201 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: 0.76 Time building geometry restraints manager: 0.93 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: 1028 1.34 - 1.46: 879 1.46 - 1.58: 1411 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 3334 Sorted by residual: bond pdb=" C VAL H 12 " pdb=" N GLN H 13 " ideal model delta sigma weight residual 1.330 1.367 -0.037 1.47e-02 4.63e+03 6.43e+00 bond pdb=" C VAL A 433 " pdb=" N ILE A 434 " ideal model delta sigma weight residual 1.330 1.303 0.027 1.26e-02 6.30e+03 4.60e+00 bond pdb=" C SER L 93 " pdb=" N THR L 94 " ideal model delta sigma weight residual 1.332 1.296 0.036 1.92e-02 2.71e+03 3.54e+00 bond pdb=" CG GLN L 89 " pdb=" CD GLN L 89 " ideal model delta sigma weight residual 1.516 1.474 0.042 2.50e-02 1.60e+03 2.81e+00 bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.447 0.051 3.10e-02 1.04e+03 2.67e+00 ... (remaining 3329 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 4293 2.11 - 4.23: 202 4.23 - 6.34: 28 6.34 - 8.46: 3 8.46 - 10.57: 3 Bond angle restraints: 4529 Sorted by residual: angle pdb=" C PHE A 486 " pdb=" N ASN A 487 " pdb=" CA ASN A 487 " ideal model delta sigma weight residual 121.54 130.56 -9.02 1.91e+00 2.74e-01 2.23e+01 angle pdb=" C GLN L 38 " pdb=" N LYS L 39 " pdb=" CA LYS L 39 " ideal model delta sigma weight residual 120.49 114.65 5.84 1.42e+00 4.96e-01 1.69e+01 angle pdb=" N VAL A 382 " pdb=" CA VAL A 382 " pdb=" C VAL A 382 " ideal model delta sigma weight residual 108.23 103.40 4.83 1.43e+00 4.89e-01 1.14e+01 angle pdb=" N MET H 103 " pdb=" CA MET H 103 " pdb=" C MET H 103 " ideal model delta sigma weight residual 112.93 108.70 4.23 1.33e+00 5.65e-01 1.01e+01 angle pdb=" C PRO A 463 " pdb=" N PHE A 464 " pdb=" CA PHE A 464 " ideal model delta sigma weight residual 123.05 127.97 -4.92 1.57e+00 4.06e-01 9.81e+00 ... (remaining 4524 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.80: 1685 9.80 - 19.60: 223 19.60 - 29.40: 43 29.40 - 39.20: 12 39.20 - 49.00: 7 Dihedral angle restraints: 1970 sinusoidal: 749 harmonic: 1221 Sorted by residual: dihedral pdb=" CA ARG H 72 " pdb=" C ARG H 72 " pdb=" N ASP H 73 " pdb=" CA ASP H 73 " ideal model delta harmonic sigma weight residual 180.00 141.51 38.49 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CA CYS A 391 " pdb=" C CYS A 391 " pdb=" N PHE A 392 " pdb=" CA PHE A 392 " ideal model delta harmonic sigma weight residual -180.00 -146.21 -33.79 0 5.00e+00 4.00e-02 4.57e+01 dihedral pdb=" CA ARG H 87 " pdb=" C ARG H 87 " pdb=" N ALA H 88 " pdb=" CA ALA H 88 " ideal model delta harmonic sigma weight residual 180.00 -151.61 -28.39 0 5.00e+00 4.00e-02 3.22e+01 ... (remaining 1967 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 306 0.047 - 0.093: 139 0.093 - 0.140: 34 0.140 - 0.187: 10 0.187 - 0.233: 1 Chirality restraints: 490 Sorted by residual: chirality pdb=" CG LEU H 79 " pdb=" CB LEU H 79 " pdb=" CD1 LEU H 79 " pdb=" CD2 LEU H 79 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CB VAL A 350 " pdb=" CA VAL A 350 " pdb=" CG1 VAL A 350 " pdb=" CG2 VAL A 350 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CB ILE H 70 " pdb=" CA ILE H 70 " pdb=" CG1 ILE H 70 " pdb=" CG2 ILE H 70 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.44e-01 ... (remaining 487 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO L 59 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 392 " -0.017 2.00e-02 2.50e+03 1.54e-02 4.12e+00 pdb=" CG PHE A 392 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 392 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 392 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 392 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 392 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 392 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR H 101 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.93e+00 pdb=" C THR H 101 " 0.034 2.00e-02 2.50e+03 pdb=" O THR H 101 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU H 102 " -0.011 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 832 2.79 - 3.32: 2933 3.32 - 3.84: 5385 3.84 - 4.37: 6236 4.37 - 4.90: 10594 Nonbonded interactions: 25980 Sorted by model distance: nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR A 369 " pdb=" O PRO A 384 " model vdw 2.283 3.040 nonbonded pdb=" OH TYR L 36 " pdb=" OE1 GLN L 89 " model vdw 2.301 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR A 393 " pdb=" OD1 ASN A 394 " model vdw 2.326 3.040 ... (remaining 25975 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 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: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.190 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 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 : 0.007 0.060 3334 Z= 0.422 Angle : 1.044 10.573 4529 Z= 0.603 Chirality : 0.057 0.233 490 Planarity : 0.007 0.052 585 Dihedral : 9.374 43.259 1178 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 0.28 % Allowed : 1.14 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -3.72 (0.36), residues: 416 helix: -4.84 (0.54), residues: 15 sheet: -2.29 (0.40), residues: 141 loop : -2.51 (0.33), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP H 47 HIS 0.005 0.002 HIS A 519 PHE 0.035 0.004 PHE A 392 TYR 0.030 0.003 TYR H 94 ARG 0.013 0.001 ARG L 61 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 115 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.6843 (mttp) cc_final: 0.6276 (tttt) REVERT: H 45 LEU cc_start: 0.7485 (mt) cc_final: 0.7000 (mt) REVERT: H 72 ARG cc_start: 0.7856 (ptt90) cc_final: 0.7263 (ptp-110) REVERT: L 4 LEU cc_start: 0.8811 (mt) cc_final: 0.8527 (mm) REVERT: L 11 LEU cc_start: 0.7856 (tt) cc_final: 0.7409 (mt) REVERT: L 82 ASP cc_start: 0.8034 (m-30) cc_final: 0.7114 (t0) REVERT: L 104 VAL cc_start: 0.8817 (t) cc_final: 0.8450 (p) outliers start: 1 outliers final: 1 residues processed: 116 average time/residue: 0.2063 time to fit residues: 27.5445 Evaluate side-chains 66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 524 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 20 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN H 35 HIS H 84 ASN H 104 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.082243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.073217 restraints weight = 14022.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.075166 restraints weight = 7506.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.076513 restraints weight = 4742.572| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3334 Z= 0.252 Angle : 0.707 8.137 4529 Z= 0.368 Chirality : 0.046 0.183 490 Planarity : 0.005 0.039 585 Dihedral : 6.787 32.346 468 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 2.56 % Allowed : 10.83 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % 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: -3.24 (0.37), residues: 416 helix: -4.33 (0.59), residues: 21 sheet: -1.59 (0.42), residues: 129 loop : -2.36 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 35 HIS 0.002 0.001 HIS H 99 PHE 0.012 0.002 PHE A 342 TYR 0.017 0.002 TYR L 49 ARG 0.007 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.6860 (mttp) cc_final: 0.6556 (tttt) REVERT: A 457 ARG cc_start: 0.6482 (ttt-90) cc_final: 0.6192 (ttt-90) REVERT: A 524 VAL cc_start: 0.8540 (OUTLIER) cc_final: 0.8272 (p) REVERT: H 72 ARG cc_start: 0.7357 (ptt90) cc_final: 0.7052 (ptp-110) REVERT: H 74 ASN cc_start: 0.7992 (p0) cc_final: 0.7746 (p0) REVERT: H 76 LYS cc_start: 0.8502 (mmmt) cc_final: 0.8288 (ptmt) REVERT: H 103 MET cc_start: 0.7532 (mmm) cc_final: 0.7307 (mmm) REVERT: L 104 VAL cc_start: 0.8714 (t) cc_final: 0.8421 (p) outliers start: 9 outliers final: 5 residues processed: 85 average time/residue: 0.1657 time to fit residues: 17.0059 Evaluate side-chains 64 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 17 ASP Chi-restraints excluded: chain L residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 5 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 0.0980 chunk 36 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.083407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.074501 restraints weight = 13467.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.076464 restraints weight = 7270.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.077752 restraints weight = 4615.273| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3334 Z= 0.187 Angle : 0.643 7.830 4529 Z= 0.328 Chirality : 0.045 0.189 490 Planarity : 0.005 0.034 585 Dihedral : 5.950 27.032 468 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.42 % Allowed : 13.68 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -2.95 (0.38), residues: 416 helix: -4.29 (0.53), residues: 21 sheet: -1.49 (0.41), residues: 137 loop : -2.08 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 35 HIS 0.003 0.001 HIS H 99 PHE 0.017 0.002 PHE A 392 TYR 0.022 0.002 TYR L 92 ARG 0.005 0.001 ARG H 16 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.6995 (mttp) cc_final: 0.6609 (tttt) REVERT: A 457 ARG cc_start: 0.6220 (ttt-90) cc_final: 0.5877 (ttt-90) REVERT: H 103 MET cc_start: 0.7599 (mmm) cc_final: 0.7319 (mmm) REVERT: L 104 VAL cc_start: 0.8478 (t) cc_final: 0.8160 (p) outliers start: 12 outliers final: 8 residues processed: 83 average time/residue: 0.1690 time to fit residues: 16.8115 Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 38 optimal weight: 6.9990 chunk 35 optimal weight: 0.0040 chunk 40 optimal weight: 0.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.083471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.074329 restraints weight = 14279.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.076149 restraints weight = 8073.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.077271 restraints weight = 5294.603| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 3334 Z= 0.247 Angle : 0.677 11.896 4529 Z= 0.345 Chirality : 0.044 0.156 490 Planarity : 0.005 0.034 585 Dihedral : 5.821 25.256 467 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 5.13 % Allowed : 17.66 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -2.70 (0.37), residues: 416 helix: -4.48 (0.64), residues: 15 sheet: -1.42 (0.39), residues: 150 loop : -1.88 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 35 HIS 0.005 0.002 HIS H 35 PHE 0.016 0.002 PHE A 392 TYR 0.022 0.002 TYR L 36 ARG 0.005 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.390 Fit side-chains revert: symmetry clash REVERT: A 457 ARG cc_start: 0.6296 (ttt-90) cc_final: 0.5944 (ttt-90) REVERT: A 492 LEU cc_start: 0.8763 (mm) cc_final: 0.8495 (mt) REVERT: L 104 VAL cc_start: 0.8474 (t) cc_final: 0.8186 (p) outliers start: 18 outliers final: 12 residues processed: 76 average time/residue: 0.1473 time to fit residues: 13.8543 Evaluate side-chains 72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.0770 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 0.0040 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 overall best weight: 2.8156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.080791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.071336 restraints weight = 14269.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.073309 restraints weight = 7738.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.074587 restraints weight = 4929.243| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3334 Z= 0.244 Angle : 0.672 10.354 4529 Z= 0.340 Chirality : 0.045 0.159 490 Planarity : 0.004 0.034 585 Dihedral : 5.648 25.469 467 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.27 % Allowed : 18.23 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -2.50 (0.37), residues: 416 helix: -4.43 (0.63), residues: 15 sheet: -1.20 (0.40), residues: 150 loop : -1.81 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP L 35 HIS 0.004 0.002 HIS H 99 PHE 0.016 0.002 PHE H 27 TYR 0.013 0.002 TYR H 53 ARG 0.005 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 62 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8835 (mm) cc_final: 0.8596 (mt) outliers start: 15 outliers final: 15 residues processed: 67 average time/residue: 0.1678 time to fit residues: 13.6971 Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 26 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 ASN L 3 GLN L 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.078986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.069343 restraints weight = 14667.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.071280 restraints weight = 8002.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.072540 restraints weight = 5146.763| |-----------------------------------------------------------------------------| r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 3334 Z= 0.328 Angle : 0.711 10.450 4529 Z= 0.365 Chirality : 0.045 0.198 490 Planarity : 0.004 0.035 585 Dihedral : 5.965 27.636 467 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 5.41 % Allowed : 18.80 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -2.46 (0.37), residues: 416 helix: -4.39 (0.65), residues: 15 sheet: -1.12 (0.40), residues: 149 loop : -1.82 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 35 HIS 0.004 0.002 HIS H 99 PHE 0.021 0.002 PHE H 27 TYR 0.018 0.002 TYR H 53 ARG 0.006 0.001 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8784 (mm) cc_final: 0.8547 (mt) outliers start: 19 outliers final: 13 residues processed: 63 average time/residue: 0.1388 time to fit residues: 11.1570 Evaluate side-chains 66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 2 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.081569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.071716 restraints weight = 14025.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.073634 restraints weight = 7771.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.074941 restraints weight = 5069.111| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3334 Z= 0.187 Angle : 0.667 12.039 4529 Z= 0.329 Chirality : 0.044 0.175 490 Planarity : 0.004 0.035 585 Dihedral : 5.372 23.219 467 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.99 % Allowed : 20.51 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.37), residues: 416 helix: -4.33 (0.68), residues: 15 sheet: -0.72 (0.42), residues: 141 loop : -1.73 (0.35), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.015 0.002 PHE A 392 TYR 0.014 0.001 TYR L 92 ARG 0.004 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 54 ASP cc_start: 0.5643 (m-30) cc_final: 0.5310 (m-30) outliers start: 14 outliers final: 11 residues processed: 66 average time/residue: 0.1361 time to fit residues: 11.3343 Evaluate side-chains 67 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.080080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.070340 restraints weight = 14143.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.072232 restraints weight = 7846.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.073465 restraints weight = 5126.316| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3334 Z= 0.274 Angle : 0.707 13.274 4529 Z= 0.354 Chirality : 0.044 0.163 490 Planarity : 0.004 0.037 585 Dihedral : 5.591 25.305 467 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.27 % Allowed : 20.80 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.38), residues: 416 helix: -4.25 (0.77), residues: 15 sheet: -0.99 (0.41), residues: 151 loop : -1.62 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP L 35 HIS 0.003 0.002 HIS H 99 PHE 0.019 0.002 PHE H 27 TYR 0.012 0.002 TYR L 49 ARG 0.004 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 15 residues processed: 63 average time/residue: 0.1323 time to fit residues: 10.5157 Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 chunk 39 optimal weight: 0.0170 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 20 optimal weight: 0.0000 chunk 36 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 overall best weight: 2.1626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.081346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.071523 restraints weight = 14143.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.073444 restraints weight = 7838.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.074743 restraints weight = 5126.531| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3334 Z= 0.218 Angle : 0.693 13.061 4529 Z= 0.340 Chirality : 0.044 0.198 490 Planarity : 0.004 0.034 585 Dihedral : 5.351 22.768 467 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.70 % Allowed : 22.22 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -2.09 (0.38), residues: 416 helix: -4.31 (0.70), residues: 15 sheet: -0.87 (0.41), residues: 151 loop : -1.55 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.014 0.002 PHE L 62 TYR 0.012 0.001 TYR L 49 ARG 0.007 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 54 ASP cc_start: 0.5578 (m-30) cc_final: 0.5273 (m-30) REVERT: L 81 GLU cc_start: 0.7517 (pm20) cc_final: 0.7299 (pm20) outliers start: 13 outliers final: 12 residues processed: 67 average time/residue: 0.1327 time to fit residues: 11.2552 Evaluate side-chains 72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 32 optimal weight: 20.0000 chunk 34 optimal weight: 0.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.081581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.072051 restraints weight = 14443.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.073812 restraints weight = 8405.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.075090 restraints weight = 5688.519| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3334 Z= 0.313 Angle : 0.742 13.273 4529 Z= 0.371 Chirality : 0.045 0.221 490 Planarity : 0.004 0.035 585 Dihedral : 5.789 25.789 467 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 3.99 % Allowed : 22.51 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -2.18 (0.38), residues: 416 helix: -4.26 (0.75), residues: 15 sheet: -0.94 (0.41), residues: 150 loop : -1.61 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP L 35 HIS 0.004 0.002 HIS H 35 PHE 0.015 0.002 PHE L 62 TYR 0.041 0.002 TYR L 92 ARG 0.006 0.001 ARG L 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 13 residues processed: 64 average time/residue: 0.1385 time to fit residues: 11.2652 Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 456 PHE Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 96 CYS Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain L residue 93 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 30 optimal weight: 30.0000 chunk 18 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.083441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.073969 restraints weight = 14483.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.075798 restraints weight = 8377.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.077055 restraints weight = 5609.446| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3334 Z= 0.213 Angle : 0.706 12.787 4529 Z= 0.345 Chirality : 0.045 0.207 490 Planarity : 0.004 0.034 585 Dihedral : 5.472 23.101 467 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.99 % Allowed : 22.51 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.39), residues: 416 helix: -4.31 (0.68), residues: 15 sheet: -0.72 (0.41), residues: 156 loop : -1.57 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP L 35 HIS 0.002 0.001 HIS H 35 PHE 0.014 0.002 PHE L 62 TYR 0.036 0.002 TYR L 92 ARG 0.006 0.000 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1387.52 seconds wall clock time: 24 minutes 51.53 seconds (1491.53 seconds total)