Starting phenix.real_space_refine on Wed Oct 9 13:31:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdf_43148/10_2024/8vdf_43148.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdf_43148/10_2024/8vdf_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdf_43148/10_2024/8vdf_43148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdf_43148/10_2024/8vdf_43148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdf_43148/10_2024/8vdf_43148.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vdf_43148/10_2024/8vdf_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-5477/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: 0.61 Conformation dependent library (CDL) restraints added in 325.4 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: 0.38 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: 0.69 Time building geometry restraints manager: 0.72 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: 2.750 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.430 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.020 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.333 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: 0.1304 time to fit residues: 8.3724 Evaluate side-chains 42 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6479 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 fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 678 MET cc_start: 0.8453 (mmt) cc_final: 0.8065 (mmt) REVERT: H 100 TYR cc_start: 0.7424 (t80) cc_final: 0.6949 (t80) outliers start: 7 outliers final: 6 residues processed: 48 average time/residue: 0.1456 time to fit residues: 8.6866 Evaluate side-chains 45 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 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 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 15 optimal weight: 0.4980 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 0.0870 chunk 30 optimal weight: 0.0050 chunk 25 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.3772 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6440 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2640 Z= 0.170 Angle : 0.513 5.622 3559 Z= 0.273 Chirality : 0.039 0.133 379 Planarity : 0.003 0.026 448 Dihedral : 4.640 19.049 348 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.46 % Allowed : 10.56 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.46), residues: 314 helix: 1.24 (0.50), residues: 91 sheet: -1.45 (0.51), residues: 87 loop : -1.24 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 36 HIS 0.001 0.001 HIS A 663 PHE 0.010 0.002 PHE H 29 TYR 0.009 0.001 TYR L 46 ARG 0.001 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 48 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 41 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 678 MET cc_start: 0.8344 (mmt) cc_final: 0.7989 (mmt) REVERT: H 100 TYR cc_start: 0.7399 (t80) cc_final: 0.6902 (t80) outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 0.1185 time to fit residues: 6.8316 Evaluate side-chains 46 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 55 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6581 moved from start: 0.2717 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= 0.251 Angle : 0.586 5.669 3559 Z= 0.311 Chirality : 0.041 0.130 379 Planarity : 0.003 0.025 448 Dihedral : 4.832 22.128 348 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.17 % Allowed : 11.97 % 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: -1.00 (0.46), residues: 314 helix: 1.42 (0.51), residues: 91 sheet: -1.64 (0.49), residues: 93 loop : -1.33 (0.53), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.010 0.003 HIS A 663 PHE 0.012 0.002 PHE H 29 TYR 0.012 0.002 TYR L 46 ARG 0.002 0.000 ARG H 64 *********************** 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 51 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 42 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 678 MET cc_start: 0.8459 (mmt) cc_final: 0.8000 (mmt) REVERT: H 100 TYR cc_start: 0.7573 (t80) cc_final: 0.7117 (t80) outliers start: 9 outliers final: 7 residues processed: 47 average time/residue: 0.1492 time to fit residues: 9.0255 Evaluate side-chains 46 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 39 time to evaluate : 0.355 ------------------------------------------------------------------------------- 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 55 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 20 optimal weight: 0.0970 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 7 optimal weight: 0.0870 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.2821 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= 0.207 Angle : 0.538 5.768 3559 Z= 0.286 Chirality : 0.040 0.130 379 Planarity : 0.003 0.024 448 Dihedral : 4.716 21.213 348 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.87 % Allowed : 12.68 % Favored : 83.45 % 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: -0.84 (0.46), residues: 314 helix: 1.80 (0.51), residues: 91 sheet: -1.79 (0.50), residues: 87 loop : -1.29 (0.52), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 583 HIS 0.005 0.001 HIS A 663 PHE 0.019 0.002 PHE H 67 TYR 0.009 0.001 TYR L 46 ARG 0.001 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 fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 678 MET cc_start: 0.8424 (mmt) cc_final: 0.7907 (mmt) REVERT: H 100 TYR cc_start: 0.7538 (t80) cc_final: 0.7101 (t80) outliers start: 11 outliers final: 6 residues processed: 48 average time/residue: 0.1091 time to fit residues: 6.7844 Evaluate side-chains 46 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 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 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 55 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 0.3980 chunk 29 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2640 Z= 0.194 Angle : 0.536 6.254 3559 Z= 0.285 Chirality : 0.039 0.129 379 Planarity : 0.003 0.024 448 Dihedral : 4.789 25.289 348 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.52 % Allowed : 13.03 % Favored : 83.45 % 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: -0.67 (0.47), residues: 314 helix: 2.09 (0.51), residues: 91 sheet: -1.87 (0.49), residues: 94 loop : -1.08 (0.54), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 583 HIS 0.001 0.000 HIS A 577 PHE 0.018 0.002 PHE H 67 TYR 0.009 0.001 TYR L 27 ARG 0.001 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 51 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 678 MET cc_start: 0.8410 (mmt) cc_final: 0.7903 (mmt) REVERT: H 100 TYR cc_start: 0.7527 (t80) cc_final: 0.7041 (t80) outliers start: 10 outliers final: 6 residues processed: 47 average time/residue: 0.1101 time to fit residues: 6.9175 Evaluate side-chains 46 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 40 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 45 ILE Chi-restraints excluded: chain L residue 55 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 0.0570 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 5 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.4898 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.3122 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= 0.203 Angle : 0.538 6.886 3559 Z= 0.289 Chirality : 0.039 0.126 379 Planarity : 0.003 0.024 448 Dihedral : 4.791 22.550 348 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.52 % Allowed : 14.08 % Favored : 82.39 % 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: -0.56 (0.48), residues: 314 helix: 2.26 (0.51), residues: 91 sheet: -2.17 (0.49), residues: 88 loop : -0.85 (0.54), residues: 135 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 0.011 0.001 PHE H 29 TYR 0.008 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 52 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 678 MET cc_start: 0.8404 (mmt) cc_final: 0.7860 (mmt) REVERT: H 82 MET cc_start: 0.5909 (mpp) cc_final: 0.5509 (mpp) REVERT: H 100 TYR cc_start: 0.7496 (t80) cc_final: 0.7125 (t80) REVERT: L 10 MET cc_start: 0.3939 (OUTLIER) cc_final: 0.1949 (mtt) REVERT: L 24 MET cc_start: 0.4967 (OUTLIER) cc_final: 0.4382 (mmt) outliers start: 10 outliers final: 8 residues processed: 47 average time/residue: 0.1034 time to fit residues: 6.4366 Evaluate side-chains 48 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 38 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 24 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 2 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.3419 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= 0.266 Angle : 0.593 6.051 3559 Z= 0.318 Chirality : 0.040 0.127 379 Planarity : 0.003 0.024 448 Dihedral : 5.044 22.492 348 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 3.52 % Allowed : 14.08 % Favored : 82.39 % 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: -0.72 (0.48), residues: 314 helix: 2.06 (0.51), residues: 92 sheet: -2.16 (0.51), residues: 91 loop : -0.95 (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 0.013 0.002 PHE H 29 TYR 0.012 0.002 TYR L 27 ARG 0.003 0.001 ARG H 66 *********************** 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 51 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 41 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: A 678 MET cc_start: 0.8414 (mmt) cc_final: 0.7840 (mmt) REVERT: H 82 MET cc_start: 0.6083 (mpp) cc_final: 0.5318 (mpp) REVERT: H 100 TYR cc_start: 0.7608 (t80) cc_final: 0.7182 (t80) REVERT: L 10 MET cc_start: 0.4061 (OUTLIER) cc_final: 0.2017 (mtt) outliers start: 10 outliers final: 7 residues processed: 46 average time/residue: 0.1290 time to fit residues: 7.5184 Evaluate side-chains 49 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 41 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 45 ILE Chi-restraints excluded: chain L residue 55 ILE Chi-restraints excluded: chain L residue 104 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 29 optimal weight: 0.2980 chunk 17 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.0980 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2640 Z= 0.193 Angle : 0.544 6.126 3559 Z= 0.293 Chirality : 0.039 0.128 379 Planarity : 0.003 0.025 448 Dihedral : 4.838 19.912 348 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.17 % Allowed : 14.79 % Favored : 82.04 % 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: -0.49 (0.48), residues: 314 helix: 2.34 (0.52), residues: 92 sheet: -2.16 (0.52), residues: 88 loop : -0.82 (0.54), residues: 134 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 0.002 PHE H 29 TYR 0.010 0.001 TYR L 27 ARG 0.002 0.000 ARG H 71 *********************** 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 48 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.311 Fit side-chains revert: symmetry clash REVERT: A 678 MET cc_start: 0.8397 (mmt) cc_final: 0.7833 (mmt) REVERT: H 100 TYR cc_start: 0.7488 (t80) cc_final: 0.7129 (t80) REVERT: L 10 MET cc_start: 0.4093 (OUTLIER) cc_final: 0.1873 (mtt) REVERT: L 24 MET cc_start: 0.5464 (OUTLIER) cc_final: 0.5000 (mmt) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.1243 time to fit residues: 6.9435 Evaluate side-chains 48 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.282 ------------------------------------------------------------------------------- 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 24 MET Chi-restraints excluded: chain L residue 45 ILE Chi-restraints excluded: chain L residue 55 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.4980 chunk 10 optimal weight: 3.9990 chunk 25 optimal weight: 0.0010 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 1 optimal weight: 0.6980 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2640 Z= 0.189 Angle : 0.557 8.068 3559 Z= 0.301 Chirality : 0.040 0.136 379 Planarity : 0.003 0.026 448 Dihedral : 4.882 19.771 348 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.17 % Allowed : 15.49 % 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: -0.45 (0.49), residues: 314 helix: 2.47 (0.52), residues: 92 sheet: -2.23 (0.52), residues: 87 loop : -0.81 (0.54), residues: 135 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 0.015 0.002 PHE H 67 TYR 0.011 0.001 TYR L 27 ARG 0.001 0.000 ARG H 64 ********************** 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 48 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 678 MET cc_start: 0.8391 (mmt) cc_final: 0.7807 (mmt) REVERT: H 100 TYR cc_start: 0.7481 (t80) cc_final: 0.7119 (t80) outliers start: 9 outliers final: 8 residues processed: 44 average time/residue: 0.1206 time to fit residues: 6.7294 Evaluate side-chains 47 residues out of total 284 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.330 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 28 optimal weight: 2.9990 chunk 16 optimal weight: 0.0030 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.4633 r_free = 0.4633 target = 0.231971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.212048 restraints weight = 3184.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.215659 restraints weight = 2169.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.218254 restraints weight = 1617.643| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 moved from start: 0.3585 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= 0.228 Angle : 0.594 7.933 3559 Z= 0.317 Chirality : 0.040 0.147 379 Planarity : 0.003 0.026 448 Dihedral : 4.959 21.070 348 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 3.17 % Allowed : 15.49 % 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: -0.56 (0.49), residues: 314 helix: 2.36 (0.52), residues: 92 sheet: -2.18 (0.51), residues: 93 loop : -0.88 (0.55), 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 0.020 0.002 PHE H 67 TYR 0.010 0.001 TYR L 27 ARG 0.002 0.000 ARG H 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1228.03 seconds wall clock time: 24 minutes 27.17 seconds (1467.17 seconds total)