Starting phenix.real_space_refine on Wed Jul 23 11:13:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cwo_30485/07_2025/7cwo_30485.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cwo_30485/07_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_30485/07_2025/7cwo_30485.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cwo_30485/07_2025/7cwo_30485.map" model { file = "/net/cci-nas-00/data/ceres_data/7cwo_30485/07_2025/7cwo_30485.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cwo_30485/07_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-5711/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: 0.80 Conformation dependent library (CDL) restraints added in 380.7 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: 0.57 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: 0.93 Time building geometry restraints manager: 0.96 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: 0.460 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: 0.030 Set scattering table: 0.030 Process input model: 14.150 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.290 ------------------------------------------------------------------------------- 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 3340 Z= 0.320 Angle : 1.044 10.573 4541 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 Details of bonding type rmsd hydrogen bonds : bond 0.17390 ( 85) hydrogen bonds : angle 13.26128 ( 201) SS BOND : bond 0.00618 ( 6) SS BOND : angle 1.11340 ( 12) covalent geometry : bond 0.00658 ( 3334) covalent geometry : angle 1.04388 ( 4529) *********************** 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 : 0.359 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: 0.1995 time to fit residues: 26.7412 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 : 0.369 ------------------------------------------------------------------------------- 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: 4.9990 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** 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 = 0.3693 r_free = 0.3693 target = 0.081238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.072197 restraints weight = 14059.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.074093 restraints weight = 7537.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.075415 restraints weight = 4782.712| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 3340 Z= 0.209 Angle : 0.752 9.810 4541 Z= 0.392 Chirality : 0.046 0.185 490 Planarity : 0.005 0.041 585 Dihedral : 7.035 32.130 468 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 17.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.13 % Allowed : 10.83 % Favored : 86.04 % 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: -3.32 (0.37), residues: 416 helix: -4.42 (0.56), residues: 21 sheet: -1.73 (0.41), residues: 135 loop : -2.36 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 35 HIS 0.003 0.002 HIS H 99 PHE 0.014 0.002 PHE A 342 TYR 0.018 0.002 TYR L 49 ARG 0.007 0.001 ARG H 67 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 85) hydrogen bonds : angle 9.49702 ( 201) SS BOND : bond 0.00435 ( 6) SS BOND : angle 3.39583 ( 12) covalent geometry : bond 0.00472 ( 3334) covalent geometry : angle 0.73196 ( 4529) *********************** 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: 11 poor density : 77 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.6882 (mttp) cc_final: 0.6560 (tttt) REVERT: A 492 LEU cc_start: 0.8879 (mm) cc_final: 0.8562 (mt) REVERT: A 524 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8443 (p) REVERT: H 72 ARG cc_start: 0.7586 (ptt90) cc_final: 0.7276 (ptp-110) REVERT: H 74 ASN cc_start: 0.8119 (p0) cc_final: 0.7862 (p0) REVERT: H 103 MET cc_start: 0.7589 (mmm) cc_final: 0.7372 (mmm) REVERT: L 104 VAL cc_start: 0.8720 (t) cc_final: 0.8428 (p) outliers start: 11 outliers final: 5 residues processed: 83 average time/residue: 0.1600 time to fit residues: 16.0706 Evaluate side-chains 66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 524 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 102 LEU 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: 8.9990 chunk 38 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 84 ASN H 105 ASN ** L 90 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 = 0.3715 r_free = 0.3715 target = 0.080209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.070827 restraints weight = 14402.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.072535 restraints weight = 8320.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.073697 restraints weight = 5613.965| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 3340 Z= 0.302 Angle : 0.793 8.030 4541 Z= 0.416 Chirality : 0.047 0.189 490 Planarity : 0.005 0.040 585 Dihedral : 7.173 33.655 468 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 21.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 5.41 % Allowed : 13.68 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % 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: -3.29 (0.38), residues: 416 helix: -4.62 (0.59), residues: 15 sheet: -1.80 (0.40), residues: 142 loop : -2.34 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 47 HIS 0.006 0.003 HIS H 35 PHE 0.020 0.003 PHE A 392 TYR 0.021 0.003 TYR H 53 ARG 0.006 0.001 ARG H 16 Details of bonding type rmsd hydrogen bonds : bond 0.04268 ( 85) hydrogen bonds : angle 9.04670 ( 201) SS BOND : bond 0.00446 ( 6) SS BOND : angle 3.24011 ( 12) covalent geometry : bond 0.00674 ( 3334) covalent geometry : angle 0.77642 ( 4529) *********************** 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 85 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8784 (mm) cc_final: 0.8505 (mt) REVERT: L 104 VAL cc_start: 0.8554 (t) cc_final: 0.8259 (p) outliers start: 19 outliers final: 10 residues processed: 77 average time/residue: 0.1614 time to fit residues: 15.0283 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 : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 525 CYS 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 85 THR Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 27 GLN L 79 GLN ** L 90 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 = 0.3657 r_free = 0.3657 target = 0.079568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.069971 restraints weight = 14360.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.071892 restraints weight = 7806.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.073227 restraints weight = 5030.847| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 3340 Z= 0.196 Angle : 0.700 7.212 4541 Z= 0.362 Chirality : 0.045 0.183 490 Planarity : 0.005 0.039 585 Dihedral : 6.404 28.273 467 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.97 % Favored : 93.03 % Rotamer: Outliers : 4.27 % Allowed : 18.80 % Favored : 76.92 % 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: -3.01 (0.38), residues: 416 helix: -4.57 (0.56), residues: 15 sheet: -1.34 (0.41), residues: 144 loop : -2.32 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP L 35 HIS 0.003 0.002 HIS H 35 PHE 0.015 0.002 PHE A 392 TYR 0.014 0.002 TYR H 53 ARG 0.003 0.000 ARG A 454 Details of bonding type rmsd hydrogen bonds : bond 0.03758 ( 85) hydrogen bonds : angle 8.42259 ( 201) SS BOND : bond 0.00437 ( 6) SS BOND : angle 2.59545 ( 12) covalent geometry : bond 0.00439 ( 3334) covalent geometry : angle 0.68761 ( 4529) *********************** 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 76 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 61 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 67 average time/residue: 0.1489 time to fit residues: 12.2870 Evaluate side-chains 65 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 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 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 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 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.0570 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 overall best weight: 2.6106 ------------------------------------------------------------------------------- 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** L 27 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.080493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.070797 restraints weight = 14299.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.072768 restraints weight = 7862.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.074074 restraints weight = 5051.575| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3340 Z= 0.165 Angle : 0.694 8.773 4541 Z= 0.356 Chirality : 0.046 0.194 490 Planarity : 0.005 0.040 585 Dihedral : 6.059 26.710 467 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 5.13 % Allowed : 19.09 % 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: -2.75 (0.38), residues: 416 helix: -4.42 (0.66), residues: 15 sheet: -1.46 (0.41), residues: 148 loop : -1.93 (0.36), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 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 0.004 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 85) hydrogen bonds : angle 8.17154 ( 201) SS BOND : bond 0.00379 ( 6) SS BOND : angle 2.28359 ( 12) covalent geometry : bond 0.00369 ( 3334) covalent geometry : angle 0.68501 ( 4529) *********************** 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 82 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 54 ASP cc_start: 0.5912 (m-30) cc_final: 0.5577 (m-30) outliers start: 18 outliers final: 12 residues processed: 71 average time/residue: 0.1494 time to fit residues: 13.0852 Evaluate side-chains 66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 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 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 6 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS ** H 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.080327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.070539 restraints weight = 14463.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.072496 restraints weight = 7870.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.073842 restraints weight = 5044.095| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.4408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3340 Z= 0.165 Angle : 0.722 11.022 4541 Z= 0.362 Chirality : 0.046 0.202 490 Planarity : 0.004 0.039 585 Dihedral : 5.932 26.001 467 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 4.27 % Allowed : 21.08 % Favored : 74.64 % 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: -2.36 (0.39), residues: 416 helix: -4.41 (0.65), residues: 15 sheet: -0.84 (0.43), residues: 141 loop : -1.88 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 35 HIS 0.004 0.002 HIS H 99 PHE 0.012 0.002 PHE A 392 TYR 0.029 0.002 TYR L 92 ARG 0.007 0.001 ARG L 96 Details of bonding type rmsd hydrogen bonds : bond 0.03543 ( 85) hydrogen bonds : angle 7.88264 ( 201) SS BOND : bond 0.00376 ( 6) SS BOND : angle 2.21359 ( 12) covalent geometry : bond 0.00378 ( 3334) covalent geometry : angle 0.71374 ( 4529) *********************** 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 74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.370 Fit side-chains revert: symmetry clash REVERT: H 54 ASP cc_start: 0.5863 (m-30) cc_final: 0.5501 (m-30) outliers start: 15 outliers final: 12 residues processed: 65 average time/residue: 0.1429 time to fit residues: 11.6423 Evaluate side-chains 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 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 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 9 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 17 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** H 99 HIS ** 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 = 0.3687 r_free = 0.3687 target = 0.081427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.071909 restraints weight = 13849.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.073868 restraints weight = 7559.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.075177 restraints weight = 4826.221| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3340 Z= 0.132 Angle : 0.699 11.118 4541 Z= 0.347 Chirality : 0.046 0.201 490 Planarity : 0.004 0.037 585 Dihedral : 5.567 23.505 467 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.70 % Allowed : 21.94 % Favored : 74.36 % 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: -2.35 (0.39), residues: 416 helix: -4.37 (0.66), residues: 15 sheet: -1.09 (0.41), residues: 151 loop : -1.70 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 35 HIS 0.003 0.001 HIS H 35 PHE 0.014 0.001 PHE A 392 TYR 0.039 0.002 TYR L 92 ARG 0.006 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03380 ( 85) hydrogen bonds : angle 7.46086 ( 201) SS BOND : bond 0.00299 ( 6) SS BOND : angle 1.97226 ( 12) covalent geometry : bond 0.00305 ( 3334) covalent geometry : angle 0.69237 ( 4529) *********************** 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 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 58 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: H 54 ASP cc_start: 0.5740 (m-30) cc_final: 0.5387 (m-30) outliers start: 13 outliers final: 12 residues processed: 63 average time/residue: 0.1473 time to fit residues: 11.5996 Evaluate side-chains 67 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 96 CYS 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 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 29 optimal weight: 0.1980 chunk 25 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.081467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.071757 restraints weight = 13895.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.073710 restraints weight = 7655.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.075008 restraints weight = 4903.433| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3340 Z= 0.134 Angle : 0.723 11.960 4541 Z= 0.355 Chirality : 0.046 0.194 490 Planarity : 0.004 0.037 585 Dihedral : 5.444 23.053 467 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.70 % Allowed : 21.94 % Favored : 74.36 % 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: -2.29 (0.38), residues: 416 helix: -4.39 (0.63), residues: 15 sheet: -1.04 (0.41), residues: 151 loop : -1.66 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP L 35 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.001 PHE A 392 TYR 0.032 0.002 TYR L 92 ARG 0.007 0.000 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03304 ( 85) hydrogen bonds : angle 7.38943 ( 201) SS BOND : bond 0.00319 ( 6) SS BOND : angle 1.86267 ( 12) covalent geometry : bond 0.00312 ( 3334) covalent geometry : angle 0.71713 ( 4529) *********************** 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 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: H 54 ASP cc_start: 0.5670 (m-30) cc_final: 0.5321 (m-30) REVERT: L 33 LEU cc_start: 0.8569 (tt) cc_final: 0.8263 (tp) REVERT: L 81 GLU cc_start: 0.7454 (pm20) cc_final: 0.7229 (pm20) outliers start: 13 outliers final: 12 residues processed: 61 average time/residue: 0.1362 time to fit residues: 10.6918 Evaluate side-chains 67 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 96 CYS 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 97 THR 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: 0.1980 chunk 39 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 3 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 17 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.084733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.075000 restraints weight = 14012.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.077011 restraints weight = 7772.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.078388 restraints weight = 5007.515| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3340 Z= 0.103 Angle : 0.704 11.498 4541 Z= 0.338 Chirality : 0.046 0.185 490 Planarity : 0.004 0.036 585 Dihedral : 4.785 17.859 467 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.56 % Allowed : 23.36 % 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: -1.99 (0.39), residues: 416 helix: -4.47 (0.53), residues: 15 sheet: -0.75 (0.40), residues: 157 loop : -1.50 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP L 35 HIS 0.001 0.000 HIS H 35 PHE 0.016 0.001 PHE A 392 TYR 0.030 0.001 TYR L 92 ARG 0.008 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.02843 ( 85) hydrogen bonds : angle 6.64940 ( 201) SS BOND : bond 0.00269 ( 6) SS BOND : angle 1.53059 ( 12) covalent geometry : bond 0.00239 ( 3334) covalent geometry : angle 0.70001 ( 4529) *********************** 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 80 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: H 34 MET cc_start: 0.7963 (tpp) cc_final: 0.7747 (tpp) REVERT: H 54 ASP cc_start: 0.5657 (m-30) cc_final: 0.5252 (m-30) REVERT: L 33 LEU cc_start: 0.8410 (tt) cc_final: 0.8118 (tp) outliers start: 9 outliers final: 8 residues processed: 72 average time/residue: 0.1457 time to fit residues: 13.0254 Evaluate side-chains 65 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 49 TYR Chi-restraints excluded: chain L residue 82 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 8.9990 chunk 30 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 24 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.081913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.072154 restraints weight = 14207.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.074065 restraints weight = 7891.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.075417 restraints weight = 5095.896| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3340 Z= 0.158 Angle : 0.750 11.225 4541 Z= 0.367 Chirality : 0.046 0.192 490 Planarity : 0.004 0.038 585 Dihedral : 5.190 20.422 467 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.28 % Allowed : 26.21 % Favored : 71.51 % 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: -1.96 (0.39), residues: 416 helix: -4.29 (0.69), residues: 15 sheet: -0.49 (0.42), residues: 147 loop : -1.66 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP L 35 HIS 0.003 0.001 HIS H 99 PHE 0.011 0.001 PHE A 392 TYR 0.038 0.002 TYR L 92 ARG 0.008 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 85) hydrogen bonds : angle 6.96590 ( 201) SS BOND : bond 0.00408 ( 6) SS BOND : angle 2.04684 ( 12) covalent geometry : bond 0.00368 ( 3334) covalent geometry : angle 0.74343 ( 4529) ********************** 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 66 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 492 LEU cc_start: 0.8775 (mm) cc_final: 0.8512 (mt) REVERT: H 54 ASP cc_start: 0.5649 (m-30) cc_final: 0.5301 (m-30) REVERT: L 33 LEU cc_start: 0.8439 (tt) cc_final: 0.8184 (tp) outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.1368 time to fit residues: 10.3746 Evaluate side-chains 60 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 L residue 20 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 49 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 = 0.3702 r_free = 0.3702 target = 0.081604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.071823 restraints weight = 14248.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.073746 restraints weight = 7924.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.074982 restraints weight = 5122.048| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3340 Z= 0.164 Angle : 0.764 12.516 4541 Z= 0.373 Chirality : 0.046 0.186 490 Planarity : 0.004 0.035 585 Dihedral : 5.357 21.038 467 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.56 % Allowed : 25.93 % Favored : 71.51 % 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: -2.07 (0.39), residues: 416 helix: -4.17 (0.75), residues: 15 sheet: -0.85 (0.40), residues: 157 loop : -1.55 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP L 35 HIS 0.003 0.001 HIS H 35 PHE 0.013 0.002 PHE H 27 TYR 0.036 0.002 TYR L 92 ARG 0.007 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03353 ( 85) hydrogen bonds : angle 7.17336 ( 201) SS BOND : bond 0.00496 ( 6) SS BOND : angle 2.11054 ( 12) covalent geometry : bond 0.00380 ( 3334) covalent geometry : angle 0.75713 ( 4529) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1491.24 seconds wall clock time: 26 minutes 54.55 seconds (1614.55 seconds total)