Starting phenix.real_space_refine on Mon Feb 10 23:04:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cwo_30485/02_2025/7cwo_30485.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cwo_30485/02_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_30485/02_2025/7cwo_30485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cwo_30485/02_2025/7cwo_30485.map" model { file = "/net/cci-nas-00/data/ceres_data/7cwo_30485/02_2025/7cwo_30485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cwo_30485/02_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-5592/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: 2.56, per 1000 atoms: 0.79 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: 0.91 Conformation dependent library (CDL) restraints added in 387.3 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: 0.38 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: 0.79 Time building geometry restraints manager: 0.94 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: 0.340 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.360 Find NCS groups from input model: 0.020 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.640 ------------------------------------------------------------------------------- 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 : 0.373 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: 0.2094 time to fit residues: 28.1536 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 : 0.361 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.073217 restraints weight = 14022.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.075177 restraints weight = 7506.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.076493 restraints weight = 4727.707| |-----------------------------------------------------------------------------| 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 : 0.368 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.6863 (mttp) cc_final: 0.6557 (tttt) REVERT: A 457 ARG cc_start: 0.6481 (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: 0.7354 (ptt90) cc_final: 0.7050 (ptp-110) REVERT: H 74 ASN cc_start: 0.7991 (p0) cc_final: 0.7744 (p0) REVERT: H 76 LYS cc_start: 0.8499 (mmmt) cc_final: 0.8287 (ptmt) REVERT: H 103 MET cc_start: 0.7532 (mmm) cc_final: 0.7307 (mmm) REVERT: L 104 VAL cc_start: 0.8713 (t) cc_final: 0.8419 (p) outliers start: 9 outliers final: 5 residues processed: 85 average time/residue: 0.1629 time to fit residues: 16.6864 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 : 0.366 ------------------------------------------------------------------------------- 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: 10.0000 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 0.0670 chunk 36 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.9324 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.082569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.073368 restraints weight = 13789.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.075334 restraints weight = 7471.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.076660 restraints weight = 4791.080| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3334 Z= 0.207 Angle : 0.650 7.952 4529 Z= 0.334 Chirality : 0.045 0.191 490 Planarity : 0.005 0.035 585 Dihedral : 6.071 27.787 468 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.70 % Allowed : 13.68 % Favored : 82.62 % 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: -2.96 (0.38), residues: 416 helix: -4.28 (0.54), residues: 21 sheet: -1.48 (0.41), residues: 137 loop : -2.10 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 35 HIS 0.003 0.002 HIS H 99 PHE 0.017 0.002 PHE A 392 TYR 0.023 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 89 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 386 LYS cc_start: 0.7020 (mttp) cc_final: 0.6640 (tttt) REVERT: A 492 LEU cc_start: 0.8801 (mm) cc_final: 0.8550 (mt) REVERT: H 103 MET cc_start: 0.7635 (mmm) cc_final: 0.7339 (mmm) REVERT: L 104 VAL cc_start: 0.8482 (t) cc_final: 0.8155 (p) outliers start: 13 outliers final: 9 residues processed: 83 average time/residue: 0.1667 time to fit residues: 16.5883 Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 14 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 17 optimal weight: 0.0010 chunk 7 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 overall best weight: 2.6790 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.083462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.074156 restraints weight = 14304.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.075990 restraints weight = 8080.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.077289 restraints weight = 5311.070| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 3334 Z= 0.248 Angle : 0.674 12.113 4529 Z= 0.344 Chirality : 0.044 0.152 490 Planarity : 0.004 0.034 585 Dihedral : 5.896 25.156 467 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.56 % Allowed : 17.95 % 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: -2.80 (0.38), residues: 416 helix: -4.18 (0.58), residues: 21 sheet: -1.45 (0.39), residues: 150 loop : -1.93 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 35 HIS 0.004 0.002 HIS H 35 PHE 0.015 0.002 PHE A 392 TYR 0.019 0.002 TYR L 36 ARG 0.004 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 79 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8744 (mm) cc_final: 0.8473 (mt) REVERT: H 103 MET cc_start: 0.7599 (mmm) cc_final: 0.7397 (mmm) REVERT: L 104 VAL cc_start: 0.8486 (t) cc_final: 0.8200 (p) outliers start: 16 outliers final: 12 residues processed: 71 average time/residue: 0.1474 time to fit residues: 13.1467 Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 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 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 27 GLN 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: 7.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 29 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 ASN ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 79 GLN ** L 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.080788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.071540 restraints weight = 14562.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.073308 restraints weight = 8270.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.074519 restraints weight = 5463.006| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 3334 Z= 0.348 Angle : 0.727 11.028 4529 Z= 0.376 Chirality : 0.045 0.161 490 Planarity : 0.005 0.035 585 Dihedral : 6.161 28.515 467 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.84 % Allowed : 17.38 % Favored : 77.78 % 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: -2.77 (0.38), residues: 416 helix: -4.19 (0.56), residues: 21 sheet: -1.27 (0.40), residues: 149 loop : -2.03 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 35 HIS 0.007 0.003 HIS H 99 PHE 0.013 0.002 PHE A 392 TYR 0.018 0.002 TYR H 53 ARG 0.007 0.001 ARG H 67 *********************** 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 79 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8713 (mm) cc_final: 0.8452 (mt) REVERT: H 103 MET cc_start: 0.7688 (mmm) cc_final: 0.7396 (mmm) outliers start: 17 outliers final: 13 residues processed: 68 average time/residue: 0.1518 time to fit residues: 12.7861 Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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 102 LEU 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 88 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 ** 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 = 0.3732 r_free = 0.3732 target = 0.081211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.071881 restraints weight = 14876.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.073658 restraints weight = 8376.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.074874 restraints weight = 5542.578| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.4358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 3334 Z= 0.309 Angle : 0.709 10.565 4529 Z= 0.364 Chirality : 0.046 0.208 490 Planarity : 0.005 0.039 585 Dihedral : 6.053 27.535 467 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.56 % Allowed : 20.51 % 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: -2.56 (0.38), residues: 416 helix: -4.39 (0.64), residues: 15 sheet: -1.18 (0.41), residues: 150 loop : -1.90 (0.36), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 35 HIS 0.004 0.002 HIS H 99 PHE 0.013 0.002 PHE A 392 TYR 0.035 0.002 TYR L 92 ARG 0.005 0.001 ARG L 24 *********************** 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 76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 60 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8725 (mm) cc_final: 0.8469 (mt) REVERT: H 103 MET cc_start: 0.7679 (mmm) cc_final: 0.7382 (mmm) outliers start: 16 outliers final: 13 residues processed: 66 average time/residue: 0.1370 time to fit residues: 11.3660 Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 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 102 LEU 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 89 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 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 = 0.3809 r_free = 0.3809 target = 0.084685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.075526 restraints weight = 14048.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.077241 restraints weight = 8085.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.078529 restraints weight = 5390.067| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3334 Z= 0.164 Angle : 0.669 12.146 4529 Z= 0.326 Chirality : 0.045 0.206 490 Planarity : 0.004 0.037 585 Dihedral : 5.220 22.063 467 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 3.42 % Allowed : 21.65 % 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: -2.30 (0.38), residues: 416 helix: -4.35 (0.64), residues: 15 sheet: -0.97 (0.41), residues: 151 loop : -1.73 (0.36), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 35 HIS 0.001 0.001 HIS H 35 PHE 0.017 0.001 PHE A 392 TYR 0.029 0.001 TYR L 92 ARG 0.004 0.001 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 83 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 54 ASP cc_start: 0.5279 (m-30) cc_final: 0.4974 (m-30) REVERT: H 103 MET cc_start: 0.7595 (mmm) cc_final: 0.7324 (mmm) REVERT: L 69 THR cc_start: 0.7567 (p) cc_final: 0.7355 (p) outliers start: 12 outliers final: 10 residues processed: 78 average time/residue: 0.1504 time to fit residues: 14.7269 Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.403 ------------------------------------------------------------------------------- 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 69 THR Chi-restraints excluded: chain H residue 96 CYS 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 89 GLN 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: 1.9990 chunk 25 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 37 optimal weight: 0.0870 chunk 26 optimal weight: 5.9990 overall best weight: 2.1964 ------------------------------------------------------------------------------- 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** H 35 HIS ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 ASN ** 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 = 0.3775 r_free = 0.3775 target = 0.083302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.073433 restraints weight = 14150.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.075344 restraints weight = 8106.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.076637 restraints weight = 5389.201| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3334 Z= 0.216 Angle : 0.696 12.584 4529 Z= 0.341 Chirality : 0.045 0.199 490 Planarity : 0.004 0.037 585 Dihedral : 5.333 22.644 467 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.13 % Allowed : 23.08 % Favored : 73.79 % 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: -2.15 (0.38), residues: 416 helix: -4.30 (0.70), residues: 15 sheet: -0.82 (0.40), residues: 157 loop : -1.66 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 35 HIS 0.003 0.001 HIS H 99 PHE 0.008 0.001 PHE A 392 TYR 0.020 0.002 TYR L 92 ARG 0.003 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 74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 54 ASP cc_start: 0.5394 (m-30) cc_final: 0.5182 (m-30) REVERT: H 103 MET cc_start: 0.7648 (mmm) cc_final: 0.7333 (mmm) REVERT: L 69 THR cc_start: 0.7681 (p) cc_final: 0.7459 (p) outliers start: 11 outliers final: 10 residues processed: 68 average time/residue: 0.1345 time to fit residues: 11.5357 Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.394 ------------------------------------------------------------------------------- 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 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 89 GLN 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: 3.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 3 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 ** 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 = 0.3785 r_free = 0.3785 target = 0.083774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.074281 restraints weight = 14521.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.076104 restraints weight = 8473.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.077391 restraints weight = 5698.493| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3334 Z= 0.208 Angle : 0.683 10.814 4529 Z= 0.343 Chirality : 0.045 0.193 490 Planarity : 0.004 0.036 585 Dihedral : 5.302 21.199 467 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.99 % Allowed : 23.08 % Favored : 72.93 % 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: -2.02 (0.39), residues: 416 helix: -4.27 (0.71), residues: 15 sheet: -0.68 (0.41), residues: 157 loop : -1.62 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP L 35 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE A 392 TYR 0.021 0.001 TYR L 92 ARG 0.008 0.001 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 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 54 ASP cc_start: 0.5428 (m-30) cc_final: 0.5114 (m-30) REVERT: H 103 MET cc_start: 0.7476 (mmm) cc_final: 0.7217 (mmm) REVERT: L 69 THR cc_start: 0.7555 (p) cc_final: 0.7312 (p) outliers start: 14 outliers final: 10 residues processed: 65 average time/residue: 0.1398 time to fit residues: 11.4857 Evaluate side-chains 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 51 ILE 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 89 GLN 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: 0.9980 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 32 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 0.8980 chunk 24 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.7582 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.084135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.074746 restraints weight = 14230.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.076537 restraints weight = 8199.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.077796 restraints weight = 5504.856| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.4981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3334 Z= 0.202 Angle : 0.711 15.128 4529 Z= 0.344 Chirality : 0.045 0.191 490 Planarity : 0.004 0.036 585 Dihedral : 5.173 21.101 467 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.85 % Allowed : 23.65 % 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: -2.00 (0.39), residues: 416 helix: -4.26 (0.72), residues: 15 sheet: -0.69 (0.41), residues: 157 loop : -1.59 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP L 35 HIS 0.003 0.001 HIS H 35 PHE 0.008 0.001 PHE A 392 TYR 0.018 0.001 TYR L 92 ARG 0.006 0.000 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 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 54 ASP cc_start: 0.5211 (m-30) cc_final: 0.4968 (m-30) REVERT: H 103 MET cc_start: 0.7528 (mmm) cc_final: 0.7235 (mmm) REVERT: L 69 THR cc_start: 0.7498 (p) cc_final: 0.7264 (p) outliers start: 10 outliers final: 10 residues processed: 64 average time/residue: 0.1537 time to fit residues: 12.1768 Evaluate side-chains 66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 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 525 CYS Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 43 LYS 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 89 GLN 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: 5.9990 chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 18 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 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 = 0.3769 r_free = 0.3769 target = 0.082490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.072974 restraints weight = 14685.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.074808 restraints weight = 8571.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.076077 restraints weight = 5739.903| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3334 Z= 0.295 Angle : 0.711 9.898 4529 Z= 0.365 Chirality : 0.046 0.196 490 Planarity : 0.004 0.036 585 Dihedral : 5.645 23.346 467 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.99 % Allowed : 23.08 % Favored : 72.93 % 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: -2.02 (0.39), residues: 416 helix: -4.21 (0.76), residues: 15 sheet: -0.60 (0.42), residues: 158 loop : -1.69 (0.36), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP L 35 HIS 0.007 0.003 HIS H 99 PHE 0.010 0.002 PHE H 29 TYR 0.016 0.002 TYR L 92 ARG 0.006 0.001 ARG L 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1324.91 seconds wall clock time: 24 minutes 30.33 seconds (1470.33 seconds total)