Starting phenix.real_space_refine on Mon Feb 10 23:46:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ru8_24699/02_2025/7ru8_24699.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru8_24699/02_2025/7ru8_24699.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ru8_24699/02_2025/7ru8_24699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru8_24699/02_2025/7ru8_24699.map" model { file = "/net/cci-nas-00/data/ceres_data/7ru8_24699/02_2025/7ru8_24699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru8_24699/02_2025/7ru8_24699.cif" } resolution = 3.8 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= -0.001 sd= 0.014 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 2031 2.51 5 N 532 2.21 5 O 620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 3198 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 956 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "C" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1388 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 9, 'TRANS': 164} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: 4.02, per 1000 atoms: 1.26 Number of scatterers: 3198 At special positions: 0 Unit cell: (56.65, 75.19, 107.12, 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 620 8.00 N 532 7.00 C 2031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 99 " - pdb=" SG CYS H 100D" distance=2.02 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 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 BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN C 343 " " NAG L 201 " - " ASN L 28 " Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 413.6 milliseconds 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 742 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 8 sheets defined 11.4% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.494A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 59 removed outlier: 5.550A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 96 through 100 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.826A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.584A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 354 through 357 Processing sheet with id=AA8, first strand: chain 'C' and resid 452 through 454 108 hydrogen bonds defined for protein. 249 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: 0.84 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 623 1.32 - 1.45: 1156 1.45 - 1.59: 1469 1.59 - 1.73: 10 1.73 - 1.87: 17 Bond restraints: 3275 Sorted by residual: bond pdb=" CB LEU C 387 " pdb=" CG LEU C 387 " ideal model delta sigma weight residual 1.530 1.634 -0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" CG PHE C 515 " pdb=" CD2 PHE C 515 " ideal model delta sigma weight residual 1.384 1.489 -0.105 2.10e-02 2.27e+03 2.51e+01 bond pdb=" CD ARG L 96 " pdb=" NE ARG L 96 " ideal model delta sigma weight residual 1.458 1.390 0.068 1.40e-02 5.10e+03 2.37e+01 bond pdb=" CG PHE C 515 " pdb=" CD1 PHE C 515 " ideal model delta sigma weight residual 1.384 1.486 -0.102 2.10e-02 2.27e+03 2.36e+01 bond pdb=" CG PHE C 429 " pdb=" CD2 PHE C 429 " ideal model delta sigma weight residual 1.384 1.486 -0.102 2.10e-02 2.27e+03 2.34e+01 ... (remaining 3270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.57: 3844 2.57 - 5.14: 506 5.14 - 7.71: 78 7.71 - 10.27: 12 10.27 - 12.84: 3 Bond angle restraints: 4443 Sorted by residual: angle pdb=" N SER L 30 " pdb=" CA SER L 30 " pdb=" C SER L 30 " ideal model delta sigma weight residual 111.28 119.73 -8.45 1.09e+00 8.42e-01 6.01e+01 angle pdb=" C SER C 383 " pdb=" N PRO C 384 " pdb=" CA PRO C 384 " ideal model delta sigma weight residual 119.56 126.92 -7.36 1.01e+00 9.80e-01 5.31e+01 angle pdb=" N ARG H 94 " pdb=" CA ARG H 94 " pdb=" C ARG H 94 " ideal model delta sigma weight residual 113.17 122.27 -9.10 1.26e+00 6.30e-01 5.21e+01 angle pdb=" C ASN C 487 " pdb=" N CYS C 488 " pdb=" CA CYS C 488 " ideal model delta sigma weight residual 121.69 134.53 -12.84 1.85e+00 2.92e-01 4.82e+01 angle pdb=" N PRO H 41 " pdb=" CA PRO H 41 " pdb=" C PRO H 41 " ideal model delta sigma weight residual 111.26 100.42 10.84 1.63e+00 3.76e-01 4.42e+01 ... (remaining 4438 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.06: 1885 17.06 - 34.12: 53 34.12 - 51.19: 21 51.19 - 68.25: 7 68.25 - 85.31: 3 Dihedral angle restraints: 1969 sinusoidal: 799 harmonic: 1170 Sorted by residual: dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 127.21 -34.21 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" N ILE H 31 " pdb=" C ILE H 31 " pdb=" CA ILE H 31 " pdb=" CB ILE H 31 " ideal model delta harmonic sigma weight residual 123.40 131.51 -8.11 0 2.50e+00 1.60e-01 1.05e+01 dihedral pdb=" C ARG L 96 " pdb=" N ARG L 96 " pdb=" CA ARG L 96 " pdb=" CB ARG L 96 " ideal model delta harmonic sigma weight residual -122.60 -114.72 -7.88 0 2.50e+00 1.60e-01 9.92e+00 ... (remaining 1966 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.103: 354 0.103 - 0.205: 97 0.205 - 0.307: 26 0.307 - 0.409: 4 0.409 - 0.511: 6 Chirality restraints: 487 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.51e+01 chirality pdb=" C1 NAG L 201 " pdb=" ND2 ASN L 28 " pdb=" C2 NAG L 201 " pdb=" O5 NAG L 201 " both_signs ideal model delta sigma weight residual False -2.40 -2.91 0.51 2.00e-01 2.50e+01 6.53e+00 chirality pdb=" CG LEU C 387 " pdb=" CB LEU C 387 " pdb=" CD1 LEU C 387 " pdb=" CD2 LEU C 387 " both_signs ideal model delta sigma weight residual False -2.59 -3.09 0.51 2.00e-01 2.50e+01 6.38e+00 ... (remaining 484 not shown) Planarity restraints: 567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN L 28 " 0.061 2.00e-02 2.50e+03 6.58e-02 5.41e+01 pdb=" CG ASN L 28 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN L 28 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN L 28 " -0.105 2.00e-02 2.50e+03 pdb=" C1 NAG L 201 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 489 " 0.086 2.00e-02 2.50e+03 4.50e-02 4.04e+01 pdb=" CG TYR C 489 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR C 489 " -0.041 2.00e-02 2.50e+03 pdb=" CD2 TYR C 489 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR C 489 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR C 489 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR C 489 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 489 " 0.062 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.077 2.00e-02 2.50e+03 3.89e-02 3.79e+01 pdb=" CG TRP H 47 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " 0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.057 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " -0.034 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " -0.049 2.00e-02 2.50e+03 ... (remaining 564 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 1160 2.86 - 3.37: 2899 3.37 - 3.88: 5523 3.88 - 4.39: 6414 4.39 - 4.90: 10245 Nonbonded interactions: 26241 Sorted by model distance: nonbonded pdb=" N VAL C 350 " pdb=" O VAL C 350 " model vdw 2.356 2.496 nonbonded pdb=" C SER C 349 " pdb=" O VAL C 350 " model vdw 2.474 3.270 nonbonded pdb=" N TYR H 32 " pdb=" O TYR H 32 " model vdw 2.478 2.496 nonbonded pdb=" N PHE C 429 " pdb=" O PHE C 429 " model vdw 2.504 2.496 nonbonded pdb=" N ALA H 40 " pdb=" O ALA H 40 " model vdw 2.504 2.496 ... (remaining 26236 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: 4.650 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.840 Find NCS groups from input model: 0.030 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: 21.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 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 : 0.022 0.125 3275 Z= 1.415 Angle : 1.867 12.843 4443 Z= 1.221 Chirality : 0.116 0.511 487 Planarity : 0.009 0.045 565 Dihedral : 10.389 85.311 1209 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.41), residues: 395 helix: -4.33 (0.37), residues: 21 sheet: 0.28 (0.44), residues: 134 loop : 0.10 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.017 TRP H 47 PHE 0.033 0.007 PHE C 429 TYR 0.086 0.009 TYR C 489 ARG 0.006 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.2506 (mttt) cc_final: 0.1758 (mtpp) REVERT: L 2 ILE cc_start: 0.7216 (mt) cc_final: 0.6844 (mt) REVERT: C 424 LYS cc_start: 0.8356 (tptt) cc_final: 0.7692 (tptt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.2167 time to fit residues: 24.7326 Evaluate side-chains 49 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 10 optimal weight: 0.0030 chunk 19 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 22 optimal weight: 0.0000 chunk 35 optimal weight: 0.9990 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN C 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.083540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.077762 restraints weight = 14722.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.079314 restraints weight = 7826.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.080318 restraints weight = 4724.933| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3275 Z= 0.231 Angle : 0.779 7.427 4443 Z= 0.419 Chirality : 0.048 0.138 487 Planarity : 0.005 0.041 565 Dihedral : 5.993 30.156 510 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.03 % Allowed : 11.92 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.43), residues: 395 helix: -3.47 (0.81), residues: 21 sheet: 0.41 (0.50), residues: 124 loop : -0.19 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP H 47 PHE 0.033 0.002 PHE L 71 TYR 0.023 0.002 TYR C 489 ARG 0.004 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.2733 (mttt) cc_final: 0.2137 (tttm) REVERT: C 353 TRP cc_start: 0.6183 (m-90) cc_final: 0.5849 (m-90) outliers start: 7 outliers final: 4 residues processed: 63 average time/residue: 0.1729 time to fit residues: 13.1365 Evaluate side-chains 51 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN C 481 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.078887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.072402 restraints weight = 14047.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.074027 restraints weight = 7537.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.075033 restraints weight = 4582.451| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3275 Z= 0.282 Angle : 0.749 6.602 4443 Z= 0.401 Chirality : 0.047 0.223 487 Planarity : 0.005 0.042 565 Dihedral : 6.581 35.939 510 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.49 % Allowed : 12.50 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.43), residues: 395 helix: -3.00 (1.18), residues: 14 sheet: 0.22 (0.50), residues: 130 loop : -0.69 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 47 PHE 0.025 0.003 PHE L 71 TYR 0.020 0.002 TYR C 489 ARG 0.006 0.001 ARG C 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 353 TRP cc_start: 0.6469 (m-90) cc_final: 0.6214 (m-90) REVERT: C 387 LEU cc_start: 0.8214 (tp) cc_final: 0.7776 (tp) outliers start: 12 outliers final: 5 residues processed: 58 average time/residue: 0.1686 time to fit residues: 11.8597 Evaluate side-chains 49 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 44 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 1 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.075158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.068714 restraints weight = 14718.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.070293 restraints weight = 7930.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.071288 restraints weight = 4824.945| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3275 Z= 0.402 Angle : 0.819 6.836 4443 Z= 0.435 Chirality : 0.049 0.140 487 Planarity : 0.005 0.046 565 Dihedral : 7.896 42.095 510 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.78 % Allowed : 13.66 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.36 (0.42), residues: 395 helix: -2.98 (1.32), residues: 14 sheet: -0.21 (0.49), residues: 127 loop : -1.18 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 47 PHE 0.033 0.003 PHE L 71 TYR 0.020 0.002 TYR C 365 ARG 0.003 0.001 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 353 TRP cc_start: 0.6889 (m-90) cc_final: 0.6662 (m-90) REVERT: C 382 VAL cc_start: 0.8187 (OUTLIER) cc_final: 0.7969 (m) REVERT: C 387 LEU cc_start: 0.8251 (tp) cc_final: 0.7968 (tp) outliers start: 13 outliers final: 8 residues processed: 51 average time/residue: 0.1455 time to fit residues: 9.2907 Evaluate side-chains 46 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 4 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 1 optimal weight: 0.0370 chunk 30 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 overall best weight: 0.8460 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.076999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.070559 restraints weight = 14408.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.072104 restraints weight = 7698.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.073085 restraints weight = 4688.739| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3275 Z= 0.253 Angle : 0.683 5.804 4443 Z= 0.364 Chirality : 0.046 0.136 487 Planarity : 0.004 0.046 565 Dihedral : 6.980 38.407 510 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 2.91 % Allowed : 15.70 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.34 (0.42), residues: 395 helix: -3.20 (0.94), residues: 22 sheet: -0.28 (0.48), residues: 132 loop : -1.01 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 47 PHE 0.020 0.002 PHE L 71 TYR 0.011 0.001 TYR C 351 ARG 0.002 0.000 ARG C 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 48 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 71 PHE cc_start: 0.5286 (t80) cc_final: 0.5077 (m-80) REVERT: L 74 THR cc_start: 0.4534 (OUTLIER) cc_final: 0.4138 (p) REVERT: C 387 LEU cc_start: 0.8311 (tp) cc_final: 0.8051 (tp) REVERT: C 418 ILE cc_start: 0.9337 (mm) cc_final: 0.9132 (tp) outliers start: 10 outliers final: 7 residues processed: 54 average time/residue: 0.1666 time to fit residues: 10.9733 Evaluate side-chains 52 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 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 = 0.3707 r_free = 0.3707 target = 0.077471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.070930 restraints weight = 14772.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.072531 restraints weight = 7816.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.073550 restraints weight = 4733.397| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.5979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3275 Z= 0.232 Angle : 0.670 6.546 4443 Z= 0.354 Chirality : 0.046 0.145 487 Planarity : 0.004 0.048 565 Dihedral : 6.743 38.571 510 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.49 % Allowed : 14.53 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.40 (0.43), residues: 395 helix: -3.28 (0.93), residues: 22 sheet: -0.26 (0.49), residues: 127 loop : -1.08 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 353 PHE 0.017 0.002 PHE L 71 TYR 0.025 0.001 TYR L 92 ARG 0.004 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 71 PHE cc_start: 0.5493 (t80) cc_final: 0.5274 (m-80) REVERT: L 74 THR cc_start: 0.4305 (OUTLIER) cc_final: 0.3940 (p) REVERT: C 387 LEU cc_start: 0.8358 (tp) cc_final: 0.8139 (tp) outliers start: 12 outliers final: 11 residues processed: 49 average time/residue: 0.1458 time to fit residues: 9.0202 Evaluate side-chains 52 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 34 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 0.1980 chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 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 = 0.3709 r_free = 0.3709 target = 0.077872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.071459 restraints weight = 14124.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.073014 restraints weight = 7443.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.074008 restraints weight = 4506.193| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.6166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3275 Z= 0.210 Angle : 0.637 5.841 4443 Z= 0.339 Chirality : 0.045 0.143 487 Planarity : 0.004 0.047 565 Dihedral : 6.501 38.045 510 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.78 % Allowed : 14.24 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.50 (0.42), residues: 395 helix: -3.44 (0.80), residues: 28 sheet: -0.16 (0.49), residues: 125 loop : -1.16 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP C 353 PHE 0.014 0.001 PHE L 71 TYR 0.018 0.001 TYR L 92 ARG 0.008 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.4304 (OUTLIER) cc_final: 0.3926 (p) REVERT: C 387 LEU cc_start: 0.8325 (tp) cc_final: 0.8066 (tp) REVERT: C 466 ARG cc_start: 0.5021 (mpt90) cc_final: 0.4820 (ttt-90) outliers start: 13 outliers final: 12 residues processed: 53 average time/residue: 0.1585 time to fit residues: 10.3199 Evaluate side-chains 54 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 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 = 0.3713 r_free = 0.3713 target = 0.077911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.071443 restraints weight = 14066.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.072996 restraints weight = 7331.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.073965 restraints weight = 4427.693| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3275 Z= 0.253 Angle : 0.673 8.568 4443 Z= 0.354 Chirality : 0.046 0.138 487 Planarity : 0.005 0.052 565 Dihedral : 6.646 38.486 510 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 4.07 % Allowed : 15.99 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.44 (0.43), residues: 395 helix: -3.43 (0.79), residues: 28 sheet: 0.09 (0.51), residues: 118 loop : -1.22 (0.39), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP C 353 PHE 0.010 0.001 PHE C 338 TYR 0.020 0.001 TYR L 92 ARG 0.009 0.001 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.4357 (OUTLIER) cc_final: 0.3933 (p) REVERT: C 387 LEU cc_start: 0.8422 (tp) cc_final: 0.8159 (tp) outliers start: 14 outliers final: 12 residues processed: 52 average time/residue: 0.1829 time to fit residues: 11.7192 Evaluate side-chains 52 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 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 = 0.3739 r_free = 0.3739 target = 0.079084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.072760 restraints weight = 14174.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.074262 restraints weight = 7549.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.075220 restraints weight = 4597.143| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.6654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3275 Z= 0.191 Angle : 0.630 8.235 4443 Z= 0.333 Chirality : 0.045 0.131 487 Planarity : 0.004 0.046 565 Dihedral : 6.247 36.546 510 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 4.07 % Allowed : 16.57 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.32 (0.43), residues: 395 helix: -3.40 (0.79), residues: 28 sheet: 0.33 (0.53), residues: 112 loop : -1.19 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 353 PHE 0.008 0.001 PHE C 429 TYR 0.015 0.001 TYR C 351 ARG 0.006 0.000 ARG C 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.4166 (OUTLIER) cc_final: 0.3842 (p) REVERT: C 468 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8612 (tp) outliers start: 14 outliers final: 11 residues processed: 52 average time/residue: 0.1623 time to fit residues: 10.4910 Evaluate side-chains 50 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.078735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.072344 restraints weight = 14115.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.073866 restraints weight = 7542.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.074819 restraints weight = 4598.013| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.6837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3275 Z= 0.208 Angle : 0.645 8.339 4443 Z= 0.340 Chirality : 0.046 0.154 487 Planarity : 0.004 0.045 565 Dihedral : 6.295 36.942 510 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.78 % Allowed : 16.57 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.41 (0.43), residues: 395 helix: -3.47 (0.68), residues: 34 sheet: 0.10 (0.51), residues: 118 loop : -1.10 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 353 PHE 0.009 0.001 PHE C 338 TYR 0.015 0.001 TYR C 351 ARG 0.005 0.000 ARG C 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 790 Ramachandran restraints generated. 395 Oldfield, 0 Emsley, 395 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.4236 (OUTLIER) cc_final: 0.3844 (p) REVERT: C 468 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8662 (tp) outliers start: 13 outliers final: 11 residues processed: 49 average time/residue: 0.1541 time to fit residues: 9.5382 Evaluate side-chains 51 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 503 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 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 = 0.3712 r_free = 0.3712 target = 0.077923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.071463 restraints weight = 14142.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.072984 restraints weight = 7603.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.073931 restraints weight = 4643.044| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.6970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3275 Z= 0.252 Angle : 0.693 8.093 4443 Z= 0.366 Chirality : 0.046 0.137 487 Planarity : 0.004 0.045 565 Dihedral : 6.558 38.176 510 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.78 % Allowed : 16.28 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.56 (0.42), residues: 395 helix: -3.42 (0.69), residues: 34 sheet: -0.01 (0.50), residues: 118 loop : -1.22 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 353 PHE 0.010 0.001 PHE C 338 TYR 0.016 0.001 TYR C 351 ARG 0.004 0.001 ARG C 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1599.54 seconds wall clock time: 29 minutes 26.61 seconds (1766.61 seconds total)