Starting phenix.real_space_refine on Mon Jan 13 14:25:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vdf_43148/01_2025/8vdf_43148.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vdf_43148/01_2025/8vdf_43148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vdf_43148/01_2025/8vdf_43148.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vdf_43148/01_2025/8vdf_43148.map" model { file = "/net/cci-nas-00/data/ceres_data/8vdf_43148/01_2025/8vdf_43148.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vdf_43148/01_2025/8vdf_43148.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 20 5.16 5 C 1637 2.51 5 N 432 2.21 5 O 495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 2584 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 888 Classifications: {'peptide': 103} Link IDs: {'TRANS': 102} Chain breaks: 3 Chain: "H" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 935 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 3, 'TRANS': 120} Chain: "L" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 761 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Time building chain proxies: 2.98, per 1000 atoms: 1.15 Number of scatterers: 2584 At special positions: 0 Unit cell: (63.8, 67.425, 76.85, 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 20 16.00 O 495 8.00 N 432 7.00 C 1637 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 601 " - pdb=" SG CYS A 614 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 85 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 277.7 milliseconds 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 594 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 5 sheets defined 33.1% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 577 through 598 Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 614 through 636 Processing helix chain 'A' and resid 652 through 657 Processing helix chain 'A' and resid 660 through 669 removed outlier: 3.697A pdb=" N VAL A 664 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 685 removed outlier: 3.575A pdb=" N TRP A 674 " --> pdb=" O LYS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 714 removed outlier: 3.715A pdb=" N ILE A 714 " --> pdb=" O GLU A 710 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.758A pdb=" N SER H 87 " --> pdb=" O ASP H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 80 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 removed outlier: 4.126A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR H 79 " --> pdb=" O SER H 70 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER H 70 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59 removed outlier: 7.162A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL H 102 " --> pdb=" O LYS H 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 59 removed outlier: 7.162A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR H 90 " --> pdb=" O THR H 107 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 12 removed outlier: 4.042A pdb=" N MET L 10 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR L 101 " --> pdb=" O TYR L 83 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR L 83 " --> pdb=" O THR L 101 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP L 82 " --> pdb=" O GLN L 35 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN L 35 " --> pdb=" O ASP L 82 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TRP L 32 " --> pdb=" O VAL L 44 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 18 through 21 removed outlier: 3.554A pdb=" N ALA L 18 " --> pdb=" O ILE L 72 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE L 72 " --> pdb=" O ALA L 18 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ILE L 20 " --> pdb=" O LEU L 70 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 327 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: 0.64 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 816 1.34 - 1.46: 666 1.46 - 1.58: 1128 1.58 - 1.70: 0 1.70 - 1.82: 30 Bond restraints: 2640 Sorted by residual: bond pdb=" CB GLN H 3 " pdb=" CG GLN H 3 " ideal model delta sigma weight residual 1.520 1.565 -0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" CB ASN L 63 " pdb=" CG ASN L 63 " ideal model delta sigma weight residual 1.516 1.551 -0.035 2.50e-02 1.60e+03 1.91e+00 bond pdb=" CG GLN H 3 " pdb=" CD GLN H 3 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.73e+00 bond pdb=" C ILE L 55 " pdb=" N PRO L 56 " ideal model delta sigma weight residual 1.330 1.346 -0.016 1.25e-02 6.40e+03 1.71e+00 bond pdb=" CB GLN L 16 " pdb=" CG GLN L 16 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.66e+00 ... (remaining 2635 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 3456 2.20 - 4.40: 84 4.40 - 6.60: 14 6.60 - 8.80: 3 8.80 - 11.00: 2 Bond angle restraints: 3559 Sorted by residual: angle pdb=" CA TYR H 100E" pdb=" CB TYR H 100E" pdb=" CG TYR H 100E" ideal model delta sigma weight residual 113.90 120.99 -7.09 1.80e+00 3.09e-01 1.55e+01 angle pdb=" C GLN L 47 " pdb=" N ASP L 48 " pdb=" CA ASP L 48 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" CB MET A 602 " pdb=" CG MET A 602 " pdb=" SD MET A 602 " ideal model delta sigma weight residual 112.70 123.70 -11.00 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CB GLU A 658 " pdb=" CG GLU A 658 " pdb=" CD GLU A 658 " ideal model delta sigma weight residual 112.60 118.08 -5.48 1.70e+00 3.46e-01 1.04e+01 angle pdb=" CB GLN H 3 " pdb=" CG GLN H 3 " pdb=" CD GLN H 3 " ideal model delta sigma weight residual 112.60 118.08 -5.48 1.70e+00 3.46e-01 1.04e+01 ... (remaining 3554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 1434 15.96 - 31.92: 89 31.92 - 47.88: 20 47.88 - 63.84: 13 63.84 - 79.79: 4 Dihedral angle restraints: 1560 sinusoidal: 630 harmonic: 930 Sorted by residual: dihedral pdb=" CB CYS A 601 " pdb=" SG CYS A 601 " pdb=" SG CYS A 614 " pdb=" CB CYS A 614 " ideal model delta sinusoidal sigma weight residual 93.00 162.33 -69.33 1 1.00e+01 1.00e-02 6.21e+01 dihedral pdb=" CB CYS H 99 " pdb=" SG CYS H 99 " pdb=" SG CYS H 100D" pdb=" CB CYS H 100D" ideal model delta sinusoidal sigma weight residual 93.00 153.60 -60.60 1 1.00e+01 1.00e-02 4.89e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 53.09 39.91 1 1.00e+01 1.00e-02 2.24e+01 ... (remaining 1557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 255 0.043 - 0.085: 85 0.085 - 0.127: 32 0.127 - 0.170: 6 0.170 - 0.212: 1 Chirality restraints: 379 Sorted by residual: chirality pdb=" CB ILE L 55 " pdb=" CA ILE L 55 " pdb=" CG1 ILE L 55 " pdb=" CG2 ILE L 55 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE H 69 " pdb=" CA ILE H 69 " pdb=" CG1 ILE H 69 " pdb=" CG2 ILE H 69 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.00e-01 chirality pdb=" CB VAL A 625 " pdb=" CA VAL A 625 " pdb=" CG1 VAL A 625 " pdb=" CG2 VAL A 625 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 376 not shown) Planarity restraints: 448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 36 " -0.017 2.00e-02 2.50e+03 1.69e-02 7.13e+00 pdb=" CG TRP H 36 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP H 36 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP H 36 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP H 36 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP H 36 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP H 36 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 36 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 36 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 36 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE L 55 " -0.036 5.00e-02 4.00e+02 5.54e-02 4.91e+00 pdb=" N PRO L 56 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO L 56 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO L 56 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG L 51 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.66e+00 pdb=" N PRO L 52 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO L 52 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 52 " -0.023 5.00e-02 4.00e+02 ... (remaining 445 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 291 2.76 - 3.29: 2361 3.29 - 3.83: 4239 3.83 - 4.36: 4873 4.36 - 4.90: 8454 Nonbonded interactions: 20218 Sorted by model distance: nonbonded pdb=" OE1 GLU A 658 " pdb=" OH TYR H 100I" model vdw 2.224 3.040 nonbonded pdb=" O GLY H 100H" pdb=" OG SER L 31 " model vdw 2.333 3.040 nonbonded pdb=" OG SER L 13 " pdb=" OE1 GLN L 16 " model vdw 2.333 3.040 nonbonded pdb=" NZ LYS A 684 " pdb=" OE1 GLU A 710 " model vdw 2.353 3.120 nonbonded pdb=" NH2 ARG L 58 " pdb=" OD2 ASP L 79 " model vdw 2.380 3.120 ... (remaining 20213 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: 2.690 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.460 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6179 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 : 0.004 0.045 2640 Z= 0.260 Angle : 0.856 10.998 3559 Z= 0.460 Chirality : 0.050 0.212 379 Planarity : 0.006 0.055 448 Dihedral : 12.535 79.795 954 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.42), residues: 314 helix: -1.12 (0.42), residues: 89 sheet: -1.38 (0.55), residues: 79 loop : -1.25 (0.49), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP H 36 HIS 0.002 0.001 HIS H 32 PHE 0.025 0.003 PHE A 657 TYR 0.010 0.002 TYR L 27 ARG 0.005 0.001 ARG L 58 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 665 MET cc_start: 0.7563 (mmp) cc_final: 0.6926 (mmt) REVERT: A 678 MET cc_start: 0.8207 (mmt) cc_final: 0.7867 (mmt) REVERT: A 683 ASN cc_start: 0.5921 (m-40) cc_final: 0.5703 (m110) REVERT: H 100 TYR cc_start: 0.7242 (t80) cc_final: 0.6525 (t80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1055 time to fit residues: 6.6834 Evaluate side-chains 42 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 603 ASN ** A 663 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN ** L 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.225895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.205074 restraints weight = 3070.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.209465 restraints weight = 1870.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.212490 restraints weight = 1283.070| |-----------------------------------------------------------------------------| r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6507 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2640 Z= 0.227 Angle : 0.596 6.180 3559 Z= 0.316 Chirality : 0.041 0.138 379 Planarity : 0.004 0.030 448 Dihedral : 5.019 21.454 348 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.46 % Allowed : 6.34 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.45), residues: 314 helix: 0.29 (0.49), residues: 92 sheet: -1.41 (0.51), residues: 91 loop : -1.13 (0.54), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 36 HIS 0.002 0.001 HIS H 32 PHE 0.014 0.002 PHE H 67 TYR 0.013 0.002 TYR L 46 ARG 0.002 0.000 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 678 MET cc_start: 0.8426 (mmt) cc_final: 0.8024 (mmt) REVERT: H 100 TYR cc_start: 0.7427 (t80) cc_final: 0.6943 (t80) REVERT: L 86 GLN cc_start: 0.7659 (tt0) cc_final: 0.7456 (tt0) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.1289 time to fit residues: 7.7195 Evaluate side-chains 45 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 55 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 26 optimal weight: 0.2980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 HIS L 16 GLN L 35 GLN L 63 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.232306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.211658 restraints weight = 3117.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.215513 restraints weight = 2068.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.218304 restraints weight = 1509.490| |-----------------------------------------------------------------------------| r_work (final): 0.4517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 2640 Z= 0.228 Angle : 0.565 5.602 3559 Z= 0.300 Chirality : 0.040 0.136 379 Planarity : 0.003 0.026 448 Dihedral : 4.913 21.224 348 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.52 % Allowed : 10.56 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.45), residues: 314 helix: 1.00 (0.50), residues: 91 sheet: -1.69 (0.49), residues: 93 loop : -1.32 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 36 HIS 0.002 0.001 HIS A 663 PHE 0.013 0.002 PHE H 29 TYR 0.012 0.001 TYR L 46 ARG 0.002 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 665 MET cc_start: 0.7647 (mmt) cc_final: 0.7229 (mmt) REVERT: A 678 MET cc_start: 0.8456 (mmt) cc_final: 0.8050 (mmt) REVERT: H 100 TYR cc_start: 0.7568 (t80) cc_final: 0.7024 (t80) outliers start: 10 outliers final: 8 residues processed: 48 average time/residue: 0.1224 time to fit residues: 7.4200 Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 24 MET Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 55 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 HIS L 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.229184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.208376 restraints weight = 3146.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.212242 restraints weight = 2077.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.214967 restraints weight = 1516.836| |-----------------------------------------------------------------------------| r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.2878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2640 Z= 0.260 Angle : 0.597 5.786 3559 Z= 0.318 Chirality : 0.041 0.131 379 Planarity : 0.003 0.025 448 Dihedral : 4.964 22.511 348 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.52 % Allowed : 11.62 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.46), residues: 314 helix: 1.24 (0.51), residues: 92 sheet: -1.82 (0.49), residues: 93 loop : -1.28 (0.53), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.010 0.003 HIS A 663 PHE 0.013 0.002 PHE H 29 TYR 0.011 0.002 TYR L 46 ARG 0.002 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 678 MET cc_start: 0.8468 (mmt) cc_final: 0.7972 (mmt) REVERT: H 100 TYR cc_start: 0.7617 (t80) cc_final: 0.7147 (t80) outliers start: 10 outliers final: 8 residues processed: 48 average time/residue: 0.1087 time to fit residues: 6.7902 Evaluate side-chains 48 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 55 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 9 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 HIS L 16 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.228997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.208216 restraints weight = 3100.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.212100 restraints weight = 2022.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.214753 restraints weight = 1466.384| |-----------------------------------------------------------------------------| r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2640 Z= 0.231 Angle : 0.575 5.845 3559 Z= 0.305 Chirality : 0.040 0.133 379 Planarity : 0.003 0.025 448 Dihedral : 4.990 24.979 348 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.58 % Allowed : 11.62 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.46), residues: 314 helix: 1.70 (0.51), residues: 91 sheet: -1.89 (0.51), residues: 87 loop : -1.34 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.003 0.001 HIS A 663 PHE 0.012 0.002 PHE H 29 TYR 0.009 0.001 TYR H 91 ARG 0.002 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 678 MET cc_start: 0.8436 (mmt) cc_final: 0.8013 (mmt) REVERT: H 100 TYR cc_start: 0.7602 (t80) cc_final: 0.7172 (t80) REVERT: L 10 MET cc_start: 0.4104 (OUTLIER) cc_final: 0.2106 (mtt) outliers start: 13 outliers final: 8 residues processed: 48 average time/residue: 0.1246 time to fit residues: 7.5409 Evaluate side-chains 49 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 10 MET Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 48 ASP Chi-restraints excluded: chain L residue 55 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 30 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 0.0030 overall best weight: 0.3768 ------------------------------------------------------------------------------- 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 = 0.4661 r_free = 0.4661 target = 0.234743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.214035 restraints weight = 3250.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.217819 restraints weight = 2166.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.220674 restraints weight = 1588.804| |-----------------------------------------------------------------------------| r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6580 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2640 Z= 0.172 Angle : 0.530 6.283 3559 Z= 0.284 Chirality : 0.039 0.128 379 Planarity : 0.003 0.024 448 Dihedral : 4.727 22.841 348 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.52 % Allowed : 13.73 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.47), residues: 314 helix: 2.11 (0.52), residues: 91 sheet: -1.86 (0.51), residues: 87 loop : -1.28 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 583 HIS 0.001 0.000 HIS A 577 PHE 0.010 0.001 PHE H 29 TYR 0.010 0.001 TYR L 27 ARG 0.002 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 678 MET cc_start: 0.8392 (mmt) cc_final: 0.7802 (mmt) REVERT: H 100 TYR cc_start: 0.7479 (t80) cc_final: 0.7100 (t80) REVERT: L 10 MET cc_start: 0.3987 (OUTLIER) cc_final: 0.1956 (mtt) outliers start: 10 outliers final: 7 residues processed: 50 average time/residue: 0.1092 time to fit residues: 7.0544 Evaluate side-chains 49 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 10 MET Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 104 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 15 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 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 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4611 r_free = 0.4611 target = 0.229066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.208307 restraints weight = 3269.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.211953 restraints weight = 2200.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.214695 restraints weight = 1623.415| |-----------------------------------------------------------------------------| r_work (final): 0.4489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6672 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2640 Z= 0.253 Angle : 0.589 6.865 3559 Z= 0.313 Chirality : 0.040 0.128 379 Planarity : 0.003 0.024 448 Dihedral : 4.911 22.210 348 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.87 % Allowed : 14.79 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.48), residues: 314 helix: 1.93 (0.52), residues: 92 sheet: -2.18 (0.50), residues: 91 loop : -0.96 (0.55), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 583 HIS 0.002 0.001 HIS A 577 PHE 0.019 0.002 PHE H 67 TYR 0.009 0.001 TYR L 27 ARG 0.002 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 678 MET cc_start: 0.8412 (mmt) cc_final: 0.7905 (mmt) REVERT: H 100 TYR cc_start: 0.7586 (t80) cc_final: 0.7160 (t80) REVERT: L 10 MET cc_start: 0.4136 (OUTLIER) cc_final: 0.2107 (mtt) outliers start: 11 outliers final: 8 residues processed: 48 average time/residue: 0.1123 time to fit residues: 6.9580 Evaluate side-chains 52 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 10 MET Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 104 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 0.0870 chunk 6 optimal weight: 0.0970 chunk 13 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 1 optimal weight: 0.4980 chunk 29 optimal weight: 0.6980 overall best weight: 0.3756 ------------------------------------------------------------------------------- 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 = 0.4644 r_free = 0.4644 target = 0.232531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.212068 restraints weight = 3142.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.216055 restraints weight = 2036.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.218853 restraints weight = 1472.151| |-----------------------------------------------------------------------------| r_work (final): 0.4531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6573 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2640 Z= 0.174 Angle : 0.533 6.315 3559 Z= 0.285 Chirality : 0.039 0.126 379 Planarity : 0.003 0.024 448 Dihedral : 4.730 18.788 348 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.82 % Allowed : 16.20 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.48), residues: 314 helix: 2.43 (0.52), residues: 91 sheet: -2.24 (0.51), residues: 85 loop : -1.01 (0.53), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 36 HIS 0.001 0.000 HIS A 577 PHE 0.015 0.002 PHE H 67 TYR 0.009 0.001 TYR L 27 ARG 0.001 0.000 ARG H 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 678 MET cc_start: 0.8388 (mmt) cc_final: 0.7876 (mmt) REVERT: H 100 TYR cc_start: 0.7452 (t80) cc_final: 0.7098 (t80) outliers start: 8 outliers final: 7 residues processed: 46 average time/residue: 0.1465 time to fit residues: 8.1975 Evaluate side-chains 47 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 72 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 11 optimal weight: 0.0270 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.233754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.213497 restraints weight = 3199.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.217271 restraints weight = 2158.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.220025 restraints weight = 1594.746| |-----------------------------------------------------------------------------| r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2640 Z= 0.194 Angle : 0.538 6.642 3559 Z= 0.287 Chirality : 0.039 0.124 379 Planarity : 0.003 0.025 448 Dihedral : 4.728 19.749 348 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.87 % Allowed : 15.49 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.49), residues: 314 helix: 2.51 (0.52), residues: 91 sheet: -2.09 (0.50), residues: 91 loop : -1.02 (0.55), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 583 HIS 0.001 0.000 HIS A 577 PHE 0.009 0.001 PHE H 29 TYR 0.009 0.001 TYR L 27 ARG 0.002 0.000 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 678 MET cc_start: 0.8406 (mmt) cc_final: 0.7882 (mmt) REVERT: H 100 TYR cc_start: 0.7503 (t80) cc_final: 0.7108 (t80) REVERT: L 10 MET cc_start: 0.4154 (OUTLIER) cc_final: 0.2059 (mtt) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 0.1320 time to fit residues: 7.7323 Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 10 MET Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4623 r_free = 0.4623 target = 0.232013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.210534 restraints weight = 3129.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.214458 restraints weight = 2083.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.217291 restraints weight = 1528.075| |-----------------------------------------------------------------------------| r_work (final): 0.4485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2640 Z= 0.235 Angle : 0.585 7.931 3559 Z= 0.314 Chirality : 0.040 0.123 379 Planarity : 0.004 0.026 448 Dihedral : 4.894 21.484 348 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.52 % Allowed : 15.49 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.49), residues: 314 helix: 2.35 (0.53), residues: 92 sheet: -2.19 (0.50), residues: 91 loop : -0.94 (0.56), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 583 HIS 0.001 0.001 HIS A 577 PHE 0.012 0.002 PHE H 67 TYR 0.009 0.001 TYR L 27 ARG 0.002 0.000 ARG H 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 628 Ramachandran restraints generated. 314 Oldfield, 0 Emsley, 314 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.278 Fit side-chains revert: symmetry clash REVERT: A 678 MET cc_start: 0.8403 (mmt) cc_final: 0.7858 (mmt) REVERT: H 82 MET cc_start: 0.6207 (mpp) cc_final: 0.5536 (mpp) REVERT: H 100 TYR cc_start: 0.7550 (t80) cc_final: 0.7131 (t80) REVERT: L 10 MET cc_start: 0.4077 (OUTLIER) cc_final: 0.1941 (mtt) outliers start: 10 outliers final: 9 residues processed: 45 average time/residue: 0.1179 time to fit residues: 6.7429 Evaluate side-chains 50 residues out of total 284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 662 PHE Chi-restraints excluded: chain A residue 663 HIS Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain L residue 10 MET Chi-restraints excluded: chain L residue 17 THR Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4641 r_free = 0.4641 target = 0.235093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.212383 restraints weight = 3201.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.215920 restraints weight = 2179.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.219054 restraints weight = 1641.530| |-----------------------------------------------------------------------------| r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2640 Z= 0.227 Angle : 0.592 7.713 3559 Z= 0.315 Chirality : 0.040 0.124 379 Planarity : 0.004 0.027 448 Dihedral : 4.899 20.970 348 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.87 % Allowed : 15.14 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.49), residues: 314 helix: 2.42 (0.52), residues: 92 sheet: -2.33 (0.49), residues: 93 loop : -0.86 (0.56), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 583 HIS 0.001 0.001 HIS A 577 PHE 0.011 0.002 PHE H 67 TYR 0.008 0.001 TYR L 27 ARG 0.001 0.000 ARG A 682 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1409.22 seconds wall clock time: 26 minutes 2.45 seconds (1562.45 seconds total)