Starting phenix.real_space_refine on Thu Jul 18 17:32:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pij_17683/07_2024/8pij_17683.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pij_17683/07_2024/8pij_17683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pij_17683/07_2024/8pij_17683.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pij_17683/07_2024/8pij_17683.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pij_17683/07_2024/8pij_17683.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pij_17683/07_2024/8pij_17683.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 10 5.16 5 C 1362 2.51 5 N 376 2.21 5 O 442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 2191 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1197 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 156} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 965 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'G3P': 1, 'WKE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.00, per 1000 atoms: 1.37 Number of scatterers: 2191 At special positions: 0 Unit cell: (71.61, 65.1, 117.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 1 15.00 O 442 8.00 N 376 7.00 C 1362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 120 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS B 24 " - pdb=" SG CYS B 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 111 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.70 Conformation dependent library (CDL) restraints added in 2.4 seconds 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 530 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 4 sheets defined 24.7% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 2 through 18 removed outlier: 3.511A pdb=" N LEU A 6 " --> pdb=" O THR A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 42 removed outlier: 4.404A pdb=" N TYR A 27 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ALA A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 removed outlier: 3.844A pdb=" N TYR A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 65 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 146 through 150 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.906A pdb=" N THR B 93 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 83 removed outlier: 3.727A pdb=" N SER A 79 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 121 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 9 removed outlier: 3.556A pdb=" N GLN B 5 " --> pdb=" O SER B 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 14 removed outlier: 3.582A pdb=" N VAL B 14 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA B 125 " --> pdb=" O ALA B 94 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILE B 36 " --> pdb=" O ILE B 53 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 51 " --> pdb=" O TRP B 38 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ARG B 40 " --> pdb=" O GLY B 49 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLY B 49 " --> pdb=" O ARG B 40 " (cutoff:3.500A) 85 hydrogen bonds defined for protein. 222 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: 0.53 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 619 1.33 - 1.45: 377 1.45 - 1.57: 1215 1.57 - 1.69: 1 1.69 - 1.81: 14 Bond restraints: 2226 Sorted by residual: bond pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " ideal model delta sigma weight residual 1.726 1.608 0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" CA MET B 116 " pdb=" C MET B 116 " ideal model delta sigma weight residual 1.524 1.491 0.033 1.25e-02 6.40e+03 6.93e+00 bond pdb=" CA VAL B 110 " pdb=" C VAL B 110 " ideal model delta sigma weight residual 1.523 1.491 0.031 1.28e-02 6.10e+03 5.91e+00 bond pdb=" CA SER B 115 " pdb=" C SER B 115 " ideal model delta sigma weight residual 1.523 1.491 0.033 1.34e-02 5.57e+03 5.89e+00 bond pdb=" CA SER B 112 " pdb=" C SER B 112 " ideal model delta sigma weight residual 1.521 1.497 0.025 1.23e-02 6.61e+03 3.99e+00 ... (remaining 2221 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.67: 40 106.67 - 113.50: 1248 113.50 - 120.33: 736 120.33 - 127.16: 976 127.16 - 133.99: 19 Bond angle restraints: 3019 Sorted by residual: angle pdb=" O1P G3P A 201 " pdb=" P G3P A 201 " pdb=" O4P G3P A 201 " ideal model delta sigma weight residual 100.65 109.90 -9.25 3.00e+00 1.11e-01 9.51e+00 angle pdb=" N ASP B 109 " pdb=" CA ASP B 109 " pdb=" CB ASP B 109 " ideal model delta sigma weight residual 111.65 107.89 3.76 1.40e+00 5.10e-01 7.20e+00 angle pdb=" CA TYR B 113 " pdb=" CB TYR B 113 " pdb=" CG TYR B 113 " ideal model delta sigma weight residual 113.90 118.11 -4.21 1.80e+00 3.09e-01 5.46e+00 angle pdb=" C PHE B 29 " pdb=" CA PHE B 29 " pdb=" CB PHE B 29 " ideal model delta sigma weight residual 110.42 114.66 -4.24 1.99e+00 2.53e-01 4.55e+00 angle pdb=" N SER B 114 " pdb=" CA SER B 114 " pdb=" C SER B 114 " ideal model delta sigma weight residual 109.50 112.74 -3.24 1.58e+00 4.01e-01 4.20e+00 ... (remaining 3014 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.62: 1217 24.62 - 49.23: 108 49.23 - 73.84: 26 73.84 - 98.46: 0 98.46 - 123.07: 2 Dihedral angle restraints: 1353 sinusoidal: 524 harmonic: 829 Sorted by residual: dihedral pdb=" C8 WKE A 202 " pdb=" C10 WKE A 202 " pdb=" C9 WKE A 202 " pdb=" O5 WKE A 202 " ideal model delta sinusoidal sigma weight residual 173.56 -63.37 -123.07 1 3.00e+01 1.11e-03 1.65e+01 dihedral pdb=" O4 WKE A 202 " pdb=" C10 WKE A 202 " pdb=" C9 WKE A 202 " pdb=" O5 WKE A 202 " ideal model delta sinusoidal sigma weight residual -63.24 56.71 -119.95 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" N ARG B 47 " pdb=" CA ARG B 47 " pdb=" CB ARG B 47 " pdb=" CG ARG B 47 " ideal model delta sinusoidal sigma weight residual -60.00 -119.62 59.62 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 1350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 185 0.023 - 0.046: 77 0.046 - 0.069: 52 0.069 - 0.093: 17 0.093 - 0.116: 18 Chirality restraints: 349 Sorted by residual: chirality pdb=" CA VAL B 81 " pdb=" N VAL B 81 " pdb=" C VAL B 81 " pdb=" CB VAL B 81 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.35e-01 chirality pdb=" CA VAL A 80 " pdb=" N VAL A 80 " pdb=" C VAL A 80 " pdb=" CB VAL A 80 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.29e-01 chirality pdb=" CA VAL A 77 " pdb=" N VAL A 77 " pdb=" C VAL A 77 " pdb=" CB VAL A 77 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 3.15e-01 ... (remaining 346 not shown) Planarity restraints: 383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 WKE A 202 " 0.036 2.00e-02 2.50e+03 2.93e-02 1.08e+01 pdb=" C8 WKE A 202 " -0.010 2.00e-02 2.50e+03 pdb=" C9 WKE A 202 " 0.027 2.00e-02 2.50e+03 pdb=" N1 WKE A 202 " -0.046 2.00e-02 2.50e+03 pdb=" O3 WKE A 202 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 108 " -0.015 2.00e-02 2.50e+03 3.00e-02 9.00e+00 pdb=" C SER B 108 " 0.052 2.00e-02 2.50e+03 pdb=" O SER B 108 " -0.020 2.00e-02 2.50e+03 pdb=" N ASP B 109 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" N WKE A 202 " -0.018 2.00e-02 2.50e+03 1.15e-02 1.66e+00 pdb=" C3 WKE A 202 " 0.014 2.00e-02 2.50e+03 pdb=" C4 WKE A 202 " -0.004 2.00e-02 2.50e+03 pdb=" C5 WKE A 202 " 0.011 2.00e-02 2.50e+03 pdb=" O1 WKE A 202 " -0.003 2.00e-02 2.50e+03 ... (remaining 380 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 365 2.76 - 3.30: 1773 3.30 - 3.83: 3372 3.83 - 4.37: 3797 4.37 - 4.90: 6913 Nonbonded interactions: 16220 Sorted by model distance: nonbonded pdb=" O ALA A 31 " pdb=" OG SER A 34 " model vdw 2.231 2.440 nonbonded pdb=" OD2 ASP A 60 " pdb=" OG SER B 108 " model vdw 2.260 2.440 nonbonded pdb=" NH2 ARG B 103 " pdb=" O1 WKE A 202 " model vdw 2.348 2.520 nonbonded pdb=" OG1 THR A 81 " pdb=" O3P G3P A 201 " model vdw 2.355 2.440 nonbonded pdb=" OG SER B 56 " pdb=" O SER B 108 " model vdw 2.356 2.440 ... (remaining 16215 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.060 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:13.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 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 0.118 2226 Z= 0.304 Angle : 0.578 9.250 3019 Z= 0.290 Chirality : 0.041 0.116 349 Planarity : 0.004 0.031 383 Dihedral : 18.971 123.074 814 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.46 % Allowed : 30.74 % Favored : 65.80 % 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: 0.25 (0.52), residues: 284 helix: 1.24 (0.72), residues: 50 sheet: 0.22 (0.59), residues: 83 loop : -0.14 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 108 HIS 0.000 0.000 HIS A 149 PHE 0.002 0.001 PHE A 119 TYR 0.018 0.001 TYR B 113 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 41 GLU cc_start: 0.8356 (tt0) cc_final: 0.8044 (tt0) REVERT: B 75 ASP cc_start: 0.8350 (t0) cc_final: 0.7405 (t0) outliers start: 8 outliers final: 5 residues processed: 62 average time/residue: 0.8143 time to fit residues: 51.8218 Evaluate side-chains 52 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 47 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8841 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 2226 Z= 0.317 Angle : 0.547 4.669 3019 Z= 0.291 Chirality : 0.043 0.152 349 Planarity : 0.003 0.024 383 Dihedral : 7.375 56.273 350 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 6.49 % Allowed : 32.90 % Favored : 60.61 % 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: 0.14 (0.52), residues: 284 helix: 1.15 (0.74), residues: 51 sheet: 0.21 (0.54), residues: 92 loop : -0.29 (0.56), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.008 0.001 PHE B 102 TYR 0.008 0.001 TYR B 118 ARG 0.002 0.000 ARG B 74 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 40 time to evaluate : 0.214 Fit side-chains REVERT: A 41 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8060 (tt0) REVERT: A 126 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8667 (ttt180) REVERT: B 47 ARG cc_start: 0.8719 (ttp-170) cc_final: 0.8493 (ttp-170) REVERT: B 75 ASP cc_start: 0.8060 (t0) cc_final: 0.7506 (t70) outliers start: 15 outliers final: 7 residues processed: 49 average time/residue: 0.9989 time to fit residues: 50.1483 Evaluate side-chains 48 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.3980 chunk 25 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8852 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2226 Z= 0.285 Angle : 0.541 6.433 3019 Z= 0.283 Chirality : 0.043 0.143 349 Planarity : 0.003 0.025 383 Dihedral : 5.511 50.849 347 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 6.93 % Allowed : 30.30 % Favored : 62.77 % 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: 0.17 (0.50), residues: 284 helix: 1.29 (0.75), residues: 51 sheet: 0.38 (0.51), residues: 87 loop : -0.42 (0.55), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE B 102 TYR 0.010 0.001 TYR B 118 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 39 time to evaluate : 0.258 Fit side-chains REVERT: A 41 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8340 (tm-30) REVERT: A 126 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8623 (ttt180) REVERT: B 75 ASP cc_start: 0.8408 (t0) cc_final: 0.7787 (t0) outliers start: 16 outliers final: 7 residues processed: 51 average time/residue: 0.9418 time to fit residues: 49.3353 Evaluate side-chains 47 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 94 SER Chi-restraints excluded: chain A residue 125 THR Chi-restraints excluded: chain A residue 126 ARG Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.9980 chunk 22 optimal weight: 0.0770 chunk 15 optimal weight: 0.0470 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 24 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- 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: 0.8784 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 2226 Z= 0.115 Angle : 0.454 4.114 3019 Z= 0.243 Chirality : 0.041 0.146 349 Planarity : 0.003 0.025 383 Dihedral : 4.681 50.743 346 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 5.63 % Allowed : 31.60 % Favored : 62.77 % 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: 0.35 (0.51), residues: 284 helix: 1.72 (0.76), residues: 51 sheet: 0.36 (0.53), residues: 77 loop : -0.29 (0.54), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.003 0.001 PHE A 119 TYR 0.006 0.001 TYR B 96 ARG 0.001 0.000 ARG B 30 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 40 time to evaluate : 0.234 Fit side-chains REVERT: A 41 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7925 (tt0) outliers start: 13 outliers final: 4 residues processed: 51 average time/residue: 0.9299 time to fit residues: 48.5566 Evaluate side-chains 44 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 39 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.8845 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2226 Z= 0.255 Angle : 0.559 7.022 3019 Z= 0.291 Chirality : 0.044 0.169 349 Planarity : 0.003 0.025 383 Dihedral : 4.914 49.986 346 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.19 % Allowed : 30.74 % Favored : 64.07 % 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: 0.35 (0.50), residues: 284 helix: 1.74 (0.74), residues: 51 sheet: 0.39 (0.54), residues: 77 loop : -0.31 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 149 PHE 0.005 0.001 PHE B 102 TYR 0.007 0.001 TYR B 96 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 38 time to evaluate : 0.228 Fit side-chains REVERT: A 41 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8403 (tm-30) outliers start: 12 outliers final: 8 residues processed: 46 average time/residue: 1.0703 time to fit residues: 50.4445 Evaluate side-chains 47 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 26 optimal weight: 7.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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: 0.8843 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2226 Z= 0.241 Angle : 0.536 5.756 3019 Z= 0.285 Chirality : 0.044 0.168 349 Planarity : 0.003 0.028 383 Dihedral : 4.885 49.737 346 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.63 % Allowed : 32.03 % Favored : 62.34 % 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: 0.37 (0.50), residues: 284 helix: 1.83 (0.75), residues: 51 sheet: 0.44 (0.55), residues: 77 loop : -0.35 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.005 0.001 PHE A 119 TYR 0.007 0.001 TYR B 96 ARG 0.003 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 37 time to evaluate : 0.190 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 46 average time/residue: 0.9634 time to fit residues: 45.3240 Evaluate side-chains 47 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 8.9990 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 0.0040 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.6796 ------------------------------------------------------------------------------- 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: 0.8826 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2226 Z= 0.183 Angle : 0.555 7.776 3019 Z= 0.287 Chirality : 0.043 0.160 349 Planarity : 0.003 0.030 383 Dihedral : 4.776 49.680 346 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.63 % Allowed : 32.47 % Favored : 61.90 % 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: 0.47 (0.51), residues: 284 helix: 1.98 (0.75), residues: 51 sheet: 0.44 (0.55), residues: 77 loop : -0.28 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE A 119 TYR 0.007 0.001 TYR B 96 ARG 0.002 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 37 time to evaluate : 0.248 Fit side-chains REVERT: A 41 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8076 (tt0) outliers start: 13 outliers final: 9 residues processed: 48 average time/residue: 0.9176 time to fit residues: 45.2092 Evaluate side-chains 46 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 37 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 22 optimal weight: 0.0030 chunk 23 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.0370 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.2074 ------------------------------------------------------------------------------- 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: 0.8810 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 2226 Z= 0.159 Angle : 0.529 5.108 3019 Z= 0.281 Chirality : 0.043 0.155 349 Planarity : 0.003 0.033 383 Dihedral : 4.699 49.438 346 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.90 % Allowed : 32.90 % Favored : 63.20 % 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: 0.61 (0.51), residues: 284 helix: 2.06 (0.76), residues: 51 sheet: 0.50 (0.55), residues: 77 loop : -0.15 (0.53), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE A 119 TYR 0.007 0.001 TYR B 96 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 36 time to evaluate : 0.256 Fit side-chains REVERT: A 41 GLU cc_start: 0.8839 (tm-30) cc_final: 0.8010 (tt0) outliers start: 9 outliers final: 7 residues processed: 43 average time/residue: 1.0105 time to fit residues: 44.5700 Evaluate side-chains 42 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 35 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.0060 chunk 23 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- 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: 0.8797 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 2226 Z= 0.153 Angle : 0.567 8.359 3019 Z= 0.287 Chirality : 0.042 0.151 349 Planarity : 0.003 0.033 383 Dihedral : 4.603 49.276 346 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.46 % Allowed : 34.63 % Favored : 61.90 % 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: 0.65 (0.51), residues: 284 helix: 2.06 (0.75), residues: 51 sheet: 0.46 (0.53), residues: 82 loop : -0.09 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE A 119 TYR 0.007 0.001 TYR B 96 ARG 0.001 0.000 ARG B 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 35 time to evaluate : 0.262 Fit side-chains REVERT: A 41 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8003 (tt0) REVERT: B 93 THR cc_start: 0.8904 (m) cc_final: 0.8621 (p) outliers start: 8 outliers final: 6 residues processed: 43 average time/residue: 0.8938 time to fit residues: 39.4140 Evaluate side-chains 41 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.0970 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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: 0.8804 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2226 Z= 0.162 Angle : 0.538 5.400 3019 Z= 0.284 Chirality : 0.042 0.150 349 Planarity : 0.003 0.033 383 Dihedral : 3.841 41.514 345 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.60 % Allowed : 35.06 % Favored : 62.34 % 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: 0.69 (0.51), residues: 284 helix: 2.12 (0.76), residues: 51 sheet: 0.51 (0.53), residues: 82 loop : -0.08 (0.54), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE A 119 TYR 0.008 0.001 TYR B 82 ARG 0.001 0.000 ARG A 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 35 time to evaluate : 0.213 Fit side-chains REVERT: A 41 GLU cc_start: 0.8835 (tm-30) cc_final: 0.7995 (tt0) REVERT: B 93 THR cc_start: 0.8896 (m) cc_final: 0.8588 (p) outliers start: 6 outliers final: 6 residues processed: 41 average time/residue: 1.0507 time to fit residues: 44.2220 Evaluate side-chains 38 residues out of total 232 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 32 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 CYS Chi-restraints excluded: chain B residue 4 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.0770 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.3120 r_free = 0.3120 target = 0.063198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.042806 restraints weight = 6508.391| |-----------------------------------------------------------------------------| r_work (start): 0.2595 rms_B_bonded: 3.15 r_work: 0.2484 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2375 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 2226 Z= 0.151 Angle : 0.585 8.625 3019 Z= 0.292 Chirality : 0.042 0.153 349 Planarity : 0.003 0.034 383 Dihedral : 3.718 41.477 345 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.60 % Allowed : 36.36 % Favored : 61.04 % 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: 0.77 (0.52), residues: 284 helix: 2.12 (0.76), residues: 51 sheet: 0.59 (0.54), residues: 82 loop : -0.02 (0.55), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 108 HIS 0.001 0.000 HIS A 54 PHE 0.004 0.001 PHE A 119 TYR 0.007 0.001 TYR B 96 ARG 0.001 0.000 ARG B 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1446.95 seconds wall clock time: 30 minutes 53.73 seconds (1853.73 seconds total)