Starting phenix.real_space_refine on Mon Feb 10 22:43:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e39_30977/02_2025/7e39_30977.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e39_30977/02_2025/7e39_30977.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e39_30977/02_2025/7e39_30977.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e39_30977/02_2025/7e39_30977.map" model { file = "/net/cci-nas-00/data/ceres_data/7e39_30977/02_2025/7e39_30977.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e39_30977/02_2025/7e39_30977.cif" } resolution = 3.7 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 15 5.16 5 C 1946 2.51 5 N 525 2.21 5 O 588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 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: 3074 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "B" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 705 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 238 Unresolved non-hydrogen dihedrals: 152 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 97 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.83, per 1000 atoms: 0.92 Number of scatterers: 3074 At special positions: 0 Unit cell: (56.16, 103.68, 76.68, 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 15 16.00 O 588 8.00 N 525 7.00 C 1946 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, 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=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 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 Links applied NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 412.3 milliseconds 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 756 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 11.4% alpha, 29.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.799A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.173A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.665A 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 438 through 443 Processing helix chain 'B' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.037A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.613A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 6 removed outlier: 6.210A pdb=" N THR B 69 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 10 through 12 removed outlier: 5.769A pdb=" N MET B 11 " --> pdb=" O LEU B 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.527A pdb=" N TYR B 49 " --> pdb=" O SER B 53 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N TYR B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU B 33 " --> pdb=" O TYR B 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.713A pdb=" N VAL C 114 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 225 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: 0.83 Time building geometry restraints manager: 0.88 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: 1003 1.34 - 1.46: 799 1.46 - 1.58: 1330 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3150 Sorted by residual: bond pdb=" CG LEU A 387 " pdb=" CD1 LEU A 387 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.45e+00 bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.26e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.424 -0.021 2.00e-02 2.50e+03 1.07e+00 bond pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " ideal model delta sigma weight residual 1.808 1.774 0.034 3.30e-02 9.18e+02 1.06e+00 bond pdb=" CG LEU A 455 " pdb=" CD2 LEU A 455 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.26e-01 ... (remaining 3145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 4093 1.62 - 3.24: 164 3.24 - 4.86: 29 4.86 - 6.48: 3 6.48 - 8.10: 3 Bond angle restraints: 4292 Sorted by residual: angle pdb=" N GLY C 111 " pdb=" CA GLY C 111 " pdb=" C GLY C 111 " ideal model delta sigma weight residual 113.18 118.81 -5.63 2.37e+00 1.78e-01 5.65e+00 angle pdb=" CA TYR B 94 " pdb=" CB TYR B 94 " pdb=" CG TYR B 94 " ideal model delta sigma weight residual 113.90 109.63 4.27 1.80e+00 3.09e-01 5.62e+00 angle pdb=" C GLN B 79 " pdb=" CA GLN B 79 " pdb=" CB GLN B 79 " ideal model delta sigma weight residual 109.26 112.71 -3.45 1.47e+00 4.63e-01 5.51e+00 angle pdb=" C GLY B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta sigma weight residual 121.87 117.62 4.25 1.83e+00 2.99e-01 5.38e+00 angle pdb=" CA LEU A 455 " pdb=" CB LEU A 455 " pdb=" CG LEU A 455 " ideal model delta sigma weight residual 116.30 124.40 -8.10 3.50e+00 8.16e-02 5.36e+00 ... (remaining 4287 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.32: 1588 14.32 - 28.63: 184 28.63 - 42.95: 52 42.95 - 57.26: 12 57.26 - 71.58: 7 Dihedral angle restraints: 1843 sinusoidal: 652 harmonic: 1191 Sorted by residual: dihedral pdb=" CA LEU B 78 " pdb=" C LEU B 78 " pdb=" N GLN B 79 " pdb=" CA GLN B 79 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA SER B 67 " pdb=" C SER B 67 " pdb=" N GLU B 68 " pdb=" CA GLU B 68 " ideal model delta harmonic sigma weight residual 180.00 155.90 24.10 0 5.00e+00 4.00e-02 2.32e+01 dihedral pdb=" CA GLN B 79 " pdb=" C GLN B 79 " pdb=" N PRO B 80 " pdb=" CA PRO B 80 " ideal model delta harmonic sigma weight residual -180.00 -156.55 -23.45 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 1840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 310 0.041 - 0.083: 104 0.083 - 0.124: 40 0.124 - 0.166: 11 0.166 - 0.207: 1 Chirality restraints: 466 Sorted by residual: chirality pdb=" C1 NAG A 601 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG A 601 " pdb=" O5 NAG A 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ILE A 358 " pdb=" N ILE A 358 " pdb=" C ILE A 358 " pdb=" CB ILE A 358 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA VAL B 43 " pdb=" N VAL B 43 " pdb=" C VAL B 43 " pdb=" CB VAL B 43 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 463 not shown) Planarity restraints: 563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 94 " -0.038 5.00e-02 4.00e+02 5.74e-02 5.27e+00 pdb=" N PRO B 95 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO B 95 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 95 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 79 " -0.032 5.00e-02 4.00e+02 4.95e-02 3.93e+00 pdb=" N PRO B 80 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 80 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 80 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 456 " 0.004 2.00e-02 2.50e+03 1.34e-02 3.14e+00 pdb=" CG PHE A 456 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 PHE A 456 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 456 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 456 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 456 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 456 " 0.001 2.00e-02 2.50e+03 ... (remaining 560 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 93 2.68 - 3.24: 3074 3.24 - 3.79: 4685 3.79 - 4.35: 6276 4.35 - 4.90: 10301 Nonbonded interactions: 24429 Sorted by model distance: nonbonded pdb=" NZ LYS B 39 " pdb=" O GLU B 81 " model vdw 2.130 3.120 nonbonded pdb=" OG SER B 63 " pdb=" OG1 THR B 74 " model vdw 2.162 3.040 nonbonded pdb=" NZ LYS B 39 " pdb=" OE2 GLU B 81 " model vdw 2.172 3.120 nonbonded pdb=" NH2 ARG A 454 " pdb=" O SER A 469 " model vdw 2.217 3.120 nonbonded pdb=" O TYR B 49 " pdb=" OG SER B 53 " model vdw 2.225 3.040 ... (remaining 24424 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: 1.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.790 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 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 : 0.005 0.040 3150 Z= 0.312 Angle : 0.768 8.104 4292 Z= 0.419 Chirality : 0.050 0.207 466 Planarity : 0.005 0.057 562 Dihedral : 14.331 71.576 1072 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.38), residues: 406 helix: -3.93 (0.60), residues: 33 sheet: -1.59 (0.43), residues: 131 loop : -2.63 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 52 HIS 0.005 0.002 HIS A 519 PHE 0.024 0.002 PHE A 456 TYR 0.023 0.002 TYR B 94 ARG 0.003 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.342 Fit side-chains REVERT: A 389 ASP cc_start: 0.7161 (t0) cc_final: 0.6787 (t0) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.1822 time to fit residues: 8.8922 Evaluate side-chains 34 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 10.0000 chunk 30 optimal weight: 0.0370 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 31 optimal weight: 30.0000 chunk 12 optimal weight: 0.1980 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.4464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.069348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.062090 restraints weight = 14323.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.063470 restraints weight = 7664.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.064378 restraints weight = 4989.091| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3150 Z= 0.260 Angle : 0.673 6.604 4292 Z= 0.353 Chirality : 0.049 0.173 466 Planarity : 0.005 0.058 562 Dihedral : 6.032 24.461 471 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 0.34 % Allowed : 9.86 % Favored : 89.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.38), residues: 406 helix: -3.76 (0.67), residues: 27 sheet: -1.56 (0.42), residues: 134 loop : -2.49 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 52 HIS 0.006 0.002 HIS A 519 PHE 0.021 0.002 PHE A 456 TYR 0.020 0.002 TYR B 94 ARG 0.003 0.001 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.369 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.1843 time to fit residues: 8.0498 Evaluate side-chains 34 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 0.0270 chunk 35 optimal weight: 50.0000 chunk 4 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 3 optimal weight: 0.5980 overall best weight: 1.2840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 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 = 0.3457 r_free = 0.3457 target = 0.070331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.063108 restraints weight = 14135.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.064508 restraints weight = 7538.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.065429 restraints weight = 4872.167| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3150 Z= 0.176 Angle : 0.597 6.788 4292 Z= 0.312 Chirality : 0.048 0.191 466 Planarity : 0.005 0.063 562 Dihedral : 5.353 23.918 471 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 2.04 % Allowed : 12.93 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.39), residues: 406 helix: -3.13 (0.94), residues: 21 sheet: -1.36 (0.43), residues: 137 loop : -2.32 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 52 HIS 0.004 0.001 HIS A 519 PHE 0.021 0.001 PHE A 456 TYR 0.016 0.001 TYR B 94 ARG 0.003 0.000 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.342 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 40 average time/residue: 0.1533 time to fit residues: 7.6682 Evaluate side-chains 38 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 20.0000 chunk 36 optimal weight: 0.0670 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 30.0000 chunk 2 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.070562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.063416 restraints weight = 14263.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.064814 restraints weight = 7480.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.065742 restraints weight = 4794.670| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3150 Z= 0.177 Angle : 0.587 8.752 4292 Z= 0.304 Chirality : 0.047 0.178 466 Planarity : 0.005 0.064 562 Dihedral : 5.105 23.506 471 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.88 % Favored : 92.12 % Rotamer: Outliers : 3.40 % Allowed : 12.59 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.40), residues: 406 helix: -2.98 (0.99), residues: 21 sheet: -1.15 (0.44), residues: 137 loop : -2.22 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 52 HIS 0.004 0.001 HIS A 519 PHE 0.012 0.001 PHE A 456 TYR 0.016 0.001 TYR B 94 ARG 0.003 0.000 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.371 Fit side-chains REVERT: A 365 TYR cc_start: 0.7459 (m-80) cc_final: 0.6846 (m-80) outliers start: 10 outliers final: 7 residues processed: 41 average time/residue: 0.1568 time to fit residues: 8.0239 Evaluate side-chains 41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 20.0000 chunk 12 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 39 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 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 = 0.3434 r_free = 0.3434 target = 0.069342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.062220 restraints weight = 14385.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.063588 restraints weight = 7802.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.064485 restraints weight = 5040.955| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3150 Z= 0.329 Angle : 0.660 7.897 4292 Z= 0.341 Chirality : 0.048 0.166 466 Planarity : 0.005 0.064 562 Dihedral : 5.652 23.622 471 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 2.38 % Allowed : 15.65 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.40), residues: 406 helix: -2.97 (1.02), residues: 21 sheet: -1.42 (0.42), residues: 145 loop : -2.20 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 52 HIS 0.005 0.002 HIS A 519 PHE 0.013 0.002 PHE A 377 TYR 0.023 0.002 TYR B 94 ARG 0.004 0.001 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.371 Fit side-chains REVERT: A 365 TYR cc_start: 0.7511 (m-80) cc_final: 0.6860 (m-80) outliers start: 7 outliers final: 6 residues processed: 37 average time/residue: 0.1729 time to fit residues: 7.9258 Evaluate side-chains 39 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 20.0000 chunk 25 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 29 optimal weight: 30.0000 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 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 = 0.3458 r_free = 0.3458 target = 0.070279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.063057 restraints weight = 14608.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.064504 restraints weight = 7684.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.065457 restraints weight = 4873.923| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3150 Z= 0.185 Angle : 0.583 8.041 4292 Z= 0.301 Chirality : 0.047 0.192 466 Planarity : 0.005 0.064 562 Dihedral : 5.118 22.868 471 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 3.40 % Allowed : 16.33 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.40), residues: 406 helix: -2.76 (1.03), residues: 21 sheet: -1.62 (0.39), residues: 164 loop : -1.96 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 52 HIS 0.004 0.001 HIS A 519 PHE 0.010 0.001 PHE A 456 TYR 0.014 0.001 TYR B 94 ARG 0.002 0.000 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.404 Fit side-chains REVERT: A 365 TYR cc_start: 0.7508 (m-80) cc_final: 0.6808 (m-80) REVERT: A 427 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7200 (t0) outliers start: 10 outliers final: 6 residues processed: 37 average time/residue: 0.1705 time to fit residues: 7.8314 Evaluate side-chains 40 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 20.0000 chunk 2 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.0370 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.3260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 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 = 0.3471 r_free = 0.3471 target = 0.070760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.063581 restraints weight = 14298.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.065009 restraints weight = 7557.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.065961 restraints weight = 4807.088| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3150 Z= 0.169 Angle : 0.569 7.466 4292 Z= 0.294 Chirality : 0.046 0.176 466 Planarity : 0.005 0.065 562 Dihedral : 4.864 22.667 471 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 4.42 % Allowed : 15.99 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.41), residues: 406 helix: -2.64 (1.05), residues: 21 sheet: -1.48 (0.39), residues: 164 loop : -1.82 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 52 HIS 0.003 0.001 HIS A 519 PHE 0.010 0.001 PHE A 377 TYR 0.014 0.001 TYR B 94 ARG 0.003 0.000 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.362 Fit side-chains REVERT: A 365 TYR cc_start: 0.7511 (m-80) cc_final: 0.6760 (m-80) REVERT: A 427 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7183 (t0) outliers start: 13 outliers final: 7 residues processed: 45 average time/residue: 0.1485 time to fit residues: 8.4541 Evaluate side-chains 40 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 20.0000 chunk 19 optimal weight: 0.0980 chunk 34 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 6 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 = 0.3452 r_free = 0.3452 target = 0.070142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.062885 restraints weight = 14266.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.064298 restraints weight = 7637.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.065238 restraints weight = 4896.051| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3150 Z= 0.242 Angle : 0.628 8.563 4292 Z= 0.325 Chirality : 0.047 0.174 466 Planarity : 0.005 0.064 562 Dihedral : 5.183 22.324 471 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 3.40 % Allowed : 17.69 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.40), residues: 406 helix: -2.65 (1.05), residues: 21 sheet: -1.45 (0.39), residues: 161 loop : -1.90 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 52 HIS 0.004 0.002 HIS A 519 PHE 0.011 0.001 PHE A 377 TYR 0.017 0.002 TYR B 94 ARG 0.002 0.001 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.347 Fit side-chains REVERT: A 365 TYR cc_start: 0.7545 (m-80) cc_final: 0.6938 (m-80) REVERT: A 427 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7153 (t0) REVERT: A 493 GLN cc_start: 0.6837 (OUTLIER) cc_final: 0.6536 (tm-30) outliers start: 10 outliers final: 7 residues processed: 37 average time/residue: 0.1286 time to fit residues: 6.3130 Evaluate side-chains 42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 20.0000 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.071341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.064127 restraints weight = 14289.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.065564 restraints weight = 7586.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.066514 restraints weight = 4816.013| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3150 Z= 0.160 Angle : 0.587 8.937 4292 Z= 0.303 Chirality : 0.046 0.183 466 Planarity : 0.004 0.065 562 Dihedral : 4.792 25.332 471 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 4.08 % Allowed : 17.35 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.41), residues: 406 helix: -2.86 (0.85), residues: 27 sheet: -1.44 (0.40), residues: 164 loop : -1.68 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 52 HIS 0.003 0.001 HIS A 519 PHE 0.010 0.001 PHE A 456 TYR 0.013 0.001 TYR B 94 ARG 0.003 0.000 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.360 Fit side-chains REVERT: A 365 TYR cc_start: 0.7483 (m-80) cc_final: 0.6838 (m-80) REVERT: A 493 GLN cc_start: 0.6712 (OUTLIER) cc_final: 0.6433 (tm-30) outliers start: 12 outliers final: 7 residues processed: 41 average time/residue: 0.1431 time to fit residues: 7.5725 Evaluate side-chains 42 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 18 optimal weight: 0.0040 chunk 1 optimal weight: 0.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.071380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.064179 restraints weight = 14063.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.065582 restraints weight = 7446.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.066536 restraints weight = 4780.083| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3150 Z= 0.168 Angle : 0.600 8.673 4292 Z= 0.310 Chirality : 0.046 0.170 466 Planarity : 0.004 0.064 562 Dihedral : 4.734 24.705 471 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 2.38 % Allowed : 18.37 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.41), residues: 406 helix: -2.74 (0.88), residues: 27 sheet: -1.41 (0.40), residues: 164 loop : -1.67 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 52 HIS 0.003 0.001 HIS B 91 PHE 0.010 0.001 PHE A 456 TYR 0.014 0.001 TYR B 94 ARG 0.002 0.000 ARG C 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 812 Ramachandran restraints generated. 406 Oldfield, 0 Emsley, 406 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.306 Fit side-chains REVERT: A 365 TYR cc_start: 0.7499 (m-80) cc_final: 0.6849 (m-80) REVERT: A 493 GLN cc_start: 0.6699 (OUTLIER) cc_final: 0.6417 (tm-30) outliers start: 7 outliers final: 6 residues processed: 36 average time/residue: 0.1333 time to fit residues: 6.3682 Evaluate side-chains 41 residues out of total 352 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 484 GLU Chi-restraints excluded: chain A residue 489 TYR Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain C residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.070847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.063551 restraints weight = 14173.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.064968 restraints weight = 7574.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.065906 restraints weight = 4853.967| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3150 Z= 0.205 Angle : 0.623 8.452 4292 Z= 0.322 Chirality : 0.047 0.170 466 Planarity : 0.005 0.065 562 Dihedral : 4.918 27.448 471 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.38 % Allowed : 18.37 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.41), residues: 406 helix: -2.43 (1.07), residues: 21 sheet: -1.45 (0.40), residues: 164 loop : -1.66 (0.42), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 52 HIS 0.003 0.002 HIS A 519 PHE 0.010 0.001 PHE A 456 TYR 0.015 0.001 TYR B 94 ARG 0.002 0.000 ARG C 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1252.08 seconds wall clock time: 23 minutes 4.85 seconds (1384.85 seconds total)