Starting phenix.real_space_refine on Wed Mar 5 18:49:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ru8_24699/03_2025/7ru8_24699.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru8_24699/03_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_24699/03_2025/7ru8_24699.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru8_24699/03_2025/7ru8_24699.map" model { file = "/net/cci-nas-00/data/ceres_data/7ru8_24699/03_2025/7ru8_24699.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru8_24699/03_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-5624/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: 4.64, per 1000 atoms: 1.45 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: 0.90 Conformation dependent library (CDL) restraints added in 480.5 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: 0.88 Time building geometry restraints manager: 1.09 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: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.420 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.300 ------------------------------------------------------------------------------- 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 : 0.387 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: 0.2132 time to fit residues: 24.3456 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 : 0.365 ------------------------------------------------------------------------------- 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 = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.077756 restraints weight = 14722.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.079311 restraints weight = 7825.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.080316 restraints weight = 4723.361| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- 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 : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 13 LYS cc_start: 0.2735 (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: 0.1717 time to fit residues: 12.9987 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 : 0.322 ------------------------------------------------------------------------------- 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: 3.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3711 r_free = 0.3711 target = 0.078077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.071698 restraints weight = 14215.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.073283 restraints weight = 7654.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.074254 restraints weight = 4660.091| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3275 Z= 0.309 Angle : 0.768 6.531 4443 Z= 0.411 Chirality : 0.048 0.245 487 Planarity : 0.005 0.042 565 Dihedral : 6.747 37.082 510 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 4.07 % Allowed : 12.79 % Favored : 83.14 % 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: -0.74 (0.43), residues: 395 helix: -3.03 (1.23), residues: 14 sheet: 0.17 (0.50), residues: 130 loop : -0.69 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 47 PHE 0.026 0.003 PHE L 71 TYR 0.020 0.002 TYR C 489 ARG 0.005 0.000 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: 14 poor density : 50 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 353 TRP cc_start: 0.6529 (m-90) cc_final: 0.6262 (m-90) REVERT: C 387 LEU cc_start: 0.8192 (tp) cc_final: 0.7782 (tp) outliers start: 14 outliers final: 8 residues processed: 57 average time/residue: 0.1619 time to fit residues: 11.3116 Evaluate side-chains 53 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS 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: 0.9990 chunk 32 optimal weight: 0.4980 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 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 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.078743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.072383 restraints weight = 14525.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.073945 restraints weight = 7912.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.074943 restraints weight = 4835.367| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3275 Z= 0.229 Angle : 0.678 6.148 4443 Z= 0.364 Chirality : 0.047 0.202 487 Planarity : 0.004 0.045 565 Dihedral : 6.460 37.853 510 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.20 % Allowed : 11.63 % Favored : 85.17 % 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: -0.96 (0.42), residues: 395 helix: -2.86 (1.23), residues: 15 sheet: -0.20 (0.48), residues: 134 loop : -0.71 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 47 PHE 0.027 0.002 PHE L 71 TYR 0.013 0.001 TYR C 489 ARG 0.002 0.000 ARG C 403 *********************** 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 61 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 387 LEU cc_start: 0.8231 (tp) cc_final: 0.7859 (tp) outliers start: 11 outliers final: 10 residues processed: 55 average time/residue: 0.1512 time to fit residues: 10.3322 Evaluate side-chains 55 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 LEU 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 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS 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: 5.9990 chunk 27 optimal weight: 0.2980 chunk 14 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 1 optimal weight: 0.1980 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.079440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.072926 restraints weight = 14362.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.074580 restraints weight = 7563.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.075603 restraints weight = 4527.820| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3275 Z= 0.201 Angle : 0.652 5.979 4443 Z= 0.350 Chirality : 0.046 0.198 487 Planarity : 0.004 0.048 565 Dihedral : 6.245 37.057 510 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.20 % Allowed : 13.95 % Favored : 82.85 % 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: -0.88 (0.43), residues: 395 helix: -2.89 (1.22), residues: 15 sheet: 0.14 (0.50), residues: 127 loop : -0.83 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP C 353 PHE 0.023 0.002 PHE L 71 TYR 0.012 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 61 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 387 LEU cc_start: 0.8174 (tp) cc_final: 0.7863 (tp) REVERT: C 468 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8521 (tp) outliers start: 11 outliers final: 8 residues processed: 54 average time/residue: 0.1714 time to fit residues: 11.2442 Evaluate side-chains 51 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.077635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.071000 restraints weight = 14826.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.072545 restraints weight = 7874.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.073544 restraints weight = 4811.967| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.5851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3275 Z= 0.304 Angle : 0.714 5.941 4443 Z= 0.382 Chirality : 0.047 0.211 487 Planarity : 0.005 0.048 565 Dihedral : 6.857 39.318 510 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 3.78 % Allowed : 13.95 % Favored : 82.27 % 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: -1.17 (0.43), residues: 395 helix: -3.11 (1.16), residues: 15 sheet: -0.18 (0.48), residues: 134 loop : -0.97 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP C 353 PHE 0.014 0.002 PHE L 71 TYR 0.017 0.002 TYR C 351 ARG 0.006 0.001 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 60 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.4580 (OUTLIER) cc_final: 0.4180 (p) REVERT: C 387 LEU cc_start: 0.8353 (tp) cc_final: 0.8096 (tp) outliers start: 13 outliers final: 10 residues processed: 53 average time/residue: 0.1837 time to fit residues: 11.8735 Evaluate side-chains 53 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS 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: 0.0010 chunk 35 optimal weight: 0.3980 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.078615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.072107 restraints weight = 14163.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.073634 restraints weight = 7527.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.074601 restraints weight = 4578.437| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3275 Z= 0.203 Angle : 0.645 5.907 4443 Z= 0.345 Chirality : 0.046 0.196 487 Planarity : 0.004 0.047 565 Dihedral : 6.294 37.309 510 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 12.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.07 % Allowed : 14.24 % Favored : 81.69 % 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: -1.13 (0.43), residues: 395 helix: -3.33 (0.87), residues: 22 sheet: 0.09 (0.50), residues: 126 loop : -0.97 (0.39), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 353 PHE 0.010 0.001 PHE L 71 TYR 0.019 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 56 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 42 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.4320 (OUTLIER) cc_final: 0.3913 (p) REVERT: C 387 LEU cc_start: 0.8329 (tp) cc_final: 0.8072 (tp) outliers start: 14 outliers final: 11 residues processed: 50 average time/residue: 0.1545 time to fit residues: 9.5625 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 : 0.351 ------------------------------------------------------------------------------- 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 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 432 CYS 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: 0.0050 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 6 optimal weight: 0.7980 chunk 16 optimal weight: 0.0670 chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 0.0270 chunk 29 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 overall best weight: 0.2190 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.080148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.073723 restraints weight = 14125.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.075308 restraints weight = 7468.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.076307 restraints weight = 4521.919| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.6360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3275 Z= 0.165 Angle : 0.613 6.259 4443 Z= 0.328 Chirality : 0.046 0.186 487 Planarity : 0.004 0.045 565 Dihedral : 5.729 34.274 510 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.78 % Allowed : 15.12 % Favored : 81.10 % 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: -0.97 (0.43), residues: 395 helix: -3.42 (0.83), residues: 22 sheet: 0.36 (0.52), residues: 117 loop : -0.90 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 PHE 0.008 0.001 PHE C 429 TYR 0.015 0.001 TYR C 351 ARG 0.007 0.000 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 59 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 74 THR cc_start: 0.3995 (OUTLIER) cc_final: 0.3649 (p) REVERT: C 387 LEU cc_start: 0.8335 (tp) cc_final: 0.8028 (tp) REVERT: C 468 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8549 (tp) outliers start: 13 outliers final: 10 residues processed: 52 average time/residue: 0.1788 time to fit residues: 11.3263 Evaluate side-chains 49 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 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 432 CYS 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: 2.9990 chunk 25 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 0.0170 chunk 13 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.079180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.072944 restraints weight = 14383.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.074434 restraints weight = 7630.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.075360 restraints weight = 4616.406| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.6472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3275 Z= 0.194 Angle : 0.623 6.033 4443 Z= 0.332 Chirality : 0.046 0.191 487 Planarity : 0.004 0.043 565 Dihedral : 5.877 35.764 510 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.20 % Allowed : 16.57 % Favored : 80.23 % 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: -1.02 (0.43), residues: 395 helix: -3.39 (0.84), residues: 22 sheet: 0.25 (0.51), residues: 117 loop : -0.88 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 PHE 0.010 0.001 PHE C 338 TYR 0.015 0.001 TYR C 351 ARG 0.007 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 48 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 2 ILE cc_start: 0.7930 (mt) cc_final: 0.7661 (mm) REVERT: L 74 THR cc_start: 0.4070 (OUTLIER) cc_final: 0.3735 (p) REVERT: C 387 LEU cc_start: 0.8307 (tp) cc_final: 0.8040 (tp) REVERT: C 468 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8580 (tp) outliers start: 11 outliers final: 9 residues processed: 42 average time/residue: 0.1515 time to fit residues: 8.0832 Evaluate side-chains 46 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 35 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 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 432 CYS 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: 0.8980 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.077736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.071489 restraints weight = 14259.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.072955 restraints weight = 7664.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.073864 restraints weight = 4667.682| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.6609 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= 0.236 Angle : 0.654 7.671 4443 Z= 0.349 Chirality : 0.046 0.194 487 Planarity : 0.004 0.043 565 Dihedral : 6.298 38.230 510 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.20 % Allowed : 17.44 % 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: -1.24 (0.43), residues: 395 helix: -3.65 (0.61), residues: 34 sheet: 0.25 (0.50), residues: 117 loop : -0.94 (0.40), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 PHE 0.010 0.001 PHE C 338 TYR 0.017 0.001 TYR L 92 ARG 0.007 0.001 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 49 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 2 ILE cc_start: 0.7978 (mt) cc_final: 0.7704 (mm) REVERT: L 74 THR cc_start: 0.4279 (OUTLIER) cc_final: 0.3951 (p) REVERT: C 387 LEU cc_start: 0.8444 (tp) cc_final: 0.8175 (tp) outliers start: 11 outliers final: 9 residues processed: 43 average time/residue: 0.1665 time to fit residues: 8.7974 Evaluate side-chains 46 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 36 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 74 THR Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain C residue 347 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 432 CYS 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: 7.9990 chunk 36 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.0070 chunk 38 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6398 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.078112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.071824 restraints weight = 14693.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.073269 restraints weight = 7867.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.074191 restraints weight = 4827.286| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.6703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3275 Z= 0.215 Angle : 0.635 7.219 4443 Z= 0.338 Chirality : 0.046 0.190 487 Planarity : 0.004 0.044 565 Dihedral : 6.102 37.388 510 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 13.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 3.49 % Allowed : 16.86 % 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: -1.19 (0.42), residues: 395 helix: -3.61 (0.63), residues: 34 sheet: 0.58 (0.53), residues: 105 loop : -1.01 (0.39), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 PHE 0.010 0.001 PHE C 338 TYR 0.014 0.001 TYR L 92 ARG 0.006 0.000 ARG C 466 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1567.84 seconds wall clock time: 28 minutes 11.99 seconds (1691.99 seconds total)