Starting phenix.real_space_refine on Tue Feb 13 03:58:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmm_32615/02_2024/7wmm_32615_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmm_32615/02_2024/7wmm_32615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmm_32615/02_2024/7wmm_32615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmm_32615/02_2024/7wmm_32615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmm_32615/02_2024/7wmm_32615_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wmm_32615/02_2024/7wmm_32615_neut_updated.pdb" } resolution = 2.6 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= 0.002 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: 6 Type Number sf(0) Gaussians Br 2 7.06 5 S 2 5.16 5 C 1650 2.51 5 N 448 2.21 5 O 514 1.98 5 F 2 1.80 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-5238/modules/chem_data/mon_lib" Total number of atoms: 2618 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "B" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "C" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "D" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "E" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "F" Number of atoms: 427 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Conformer: "B" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} bond proxies already assigned to first conformer: 416 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'1KI': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N ASER A 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 42 " occ=0.50 residue: pdb=" N ASER B 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER B 42 " occ=0.50 residue: pdb=" N ASER C 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER C 42 " occ=0.50 residue: pdb=" N ASER D 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER D 42 " occ=0.50 residue: pdb=" N ASER E 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER E 42 " occ=0.50 residue: pdb=" N ASER F 42 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER F 42 " occ=0.50 Time building chain proxies: 2.79, per 1000 atoms: 1.07 Number of scatterers: 2618 At special positions: 0 Unit cell: (98.77, 105.41, 30.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Br 2 34.99 S 2 16.00 F 2 9.00 O 514 8.00 N 448 7.00 C 1650 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=0, symmetry=0 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 978.5 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 0 sheets defined 0.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... No hydrogen bonds 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: 0.00 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.37: 850 1.37 - 1.51: 864 1.51 - 1.66: 922 1.66 - 1.80: 2 1.80 - 1.94: 2 Bond restraints: 2640 Sorted by residual: bond pdb=" C16 1KI C 201 " pdb=" S27 1KI C 201 " ideal model delta sigma weight residual 1.770 1.668 0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C18 1KI A 201 " pdb=" C19 1KI A 201 " ideal model delta sigma weight residual 1.454 1.555 -0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C16 1KI A 201 " pdb=" S27 1KI A 201 " ideal model delta sigma weight residual 1.770 1.669 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C18 1KI C 201 " pdb=" C19 1KI C 201 " ideal model delta sigma weight residual 1.454 1.554 -0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" C16 1KI A 201 " pdb=" N15 1KI A 201 " ideal model delta sigma weight residual 1.303 1.396 -0.093 2.00e-02 2.50e+03 2.18e+01 ... (remaining 2635 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.14: 4 105.14 - 111.84: 1490 111.84 - 118.54: 715 118.54 - 125.23: 1361 125.23 - 131.93: 10 Bond angle restraints: 3580 Sorted by residual: angle pdb=" C17 1KI C 201 " pdb=" C18 1KI C 201 " pdb=" C19 1KI C 201 " ideal model delta sigma weight residual 126.82 103.75 23.07 3.00e+00 1.11e-01 5.91e+01 angle pdb=" C17 1KI A 201 " pdb=" C18 1KI A 201 " pdb=" C19 1KI A 201 " ideal model delta sigma weight residual 126.82 103.76 23.06 3.00e+00 1.11e-01 5.91e+01 angle pdb=" C13 1KI C 201 " pdb=" S27 1KI C 201 " pdb=" C16 1KI C 201 " ideal model delta sigma weight residual 89.32 98.45 -9.13 3.00e+00 1.11e-01 9.27e+00 angle pdb=" C13 1KI A 201 " pdb=" S27 1KI A 201 " pdb=" C16 1KI A 201 " ideal model delta sigma weight residual 89.32 98.44 -9.12 3.00e+00 1.11e-01 9.25e+00 angle pdb=" C05 1KI A 201 " pdb=" N04 1KI A 201 " pdb=" C11 1KI A 201 " ideal model delta sigma weight residual 112.35 119.89 -7.54 3.00e+00 1.11e-01 6.32e+00 ... (remaining 3575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 1449 16.30 - 32.60: 53 32.60 - 48.90: 17 48.90 - 65.20: 7 65.20 - 81.50: 6 Dihedral angle restraints: 1532 sinusoidal: 518 harmonic: 1014 Sorted by residual: dihedral pdb=" CB GLU D 46 " pdb=" CG GLU D 46 " pdb=" CD GLU D 46 " pdb=" OE1 GLU D 46 " ideal model delta sinusoidal sigma weight residual 0.00 81.50 -81.50 1 3.00e+01 1.11e-03 9.09e+00 dihedral pdb=" CB GLU C 46 " pdb=" CG GLU C 46 " pdb=" CD GLU C 46 " pdb=" OE1 GLU C 46 " ideal model delta sinusoidal sigma weight residual 0.00 81.47 -81.47 1 3.00e+01 1.11e-03 9.09e+00 dihedral pdb=" CB GLU F 46 " pdb=" CG GLU F 46 " pdb=" CD GLU F 46 " pdb=" OE1 GLU F 46 " ideal model delta sinusoidal sigma weight residual 0.00 81.40 -81.40 1 3.00e+01 1.11e-03 9.07e+00 ... (remaining 1529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 158 0.025 - 0.049: 182 0.049 - 0.074: 41 0.074 - 0.099: 18 0.099 - 0.123: 63 Chirality restraints: 462 Sorted by residual: chirality pdb=" CA VAL F 49 " pdb=" N VAL F 49 " pdb=" C VAL F 49 " pdb=" CB VAL F 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA VAL D 49 " pdb=" N VAL D 49 " pdb=" C VAL D 49 " pdb=" CB VAL D 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 459 not shown) Planarity restraints: 440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 50 " 0.005 2.00e-02 2.50e+03 5.43e-03 4.42e-01 pdb=" CG HIS A 50 " -0.012 2.00e-02 2.50e+03 pdb=" ND1 HIS A 50 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS A 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS A 50 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS A 50 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 50 " 0.005 2.00e-02 2.50e+03 5.32e-03 4.25e-01 pdb=" CG HIS B 50 " -0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS B 50 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS B 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS B 50 " -0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS B 50 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 50 " 0.005 2.00e-02 2.50e+03 5.15e-03 3.98e-01 pdb=" CG HIS E 50 " -0.011 2.00e-02 2.50e+03 pdb=" ND1 HIS E 50 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 HIS E 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS E 50 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS E 50 " 0.002 2.00e-02 2.50e+03 ... (remaining 437 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 812 2.87 - 3.38: 2181 3.38 - 3.88: 4359 3.88 - 4.39: 4421 4.39 - 4.90: 9021 Nonbonded interactions: 20794 Sorted by model distance: nonbonded pdb=" OE1 GLU A 46 " pdb=" NZ LYS E 80 " model vdw 2.361 2.520 nonbonded pdb=" NZ LYS A 80 " pdb=" OE1 GLU B 46 " model vdw 2.366 2.520 nonbonded pdb=" OE1 GLU C 46 " pdb=" NZ LYS F 80 " model vdw 2.377 2.520 nonbonded pdb=" NZ LYS C 80 " pdb=" OE1 GLU D 46 " model vdw 2.378 2.520 nonbonded pdb=" OE1 GLU A 83 " pdb=" F10 1KI A 201 " model vdw 2.458 2.390 ... (remaining 20789 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 37 through 41 or resid 43 through 97)) selection = (chain 'B' and (resid 37 through 41 or resid 43 through 97)) selection = (chain 'C' and (resid 37 through 41 or resid 43 through 97)) selection = (chain 'D' and (resid 37 through 41 or resid 43 through 97)) selection = (chain 'E' and (resid 37 through 41 or resid 43 through 97)) selection = (chain 'F' and (resid 37 through 41 or resid 43 through 97)) } 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=0.50 max=1.00 mean=0.99 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: 1.900 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: 8.920 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.740 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 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 : 0.008 0.102 2640 Z= 0.410 Angle : 0.859 23.070 3580 Z= 0.370 Chirality : 0.053 0.123 462 Planarity : 0.002 0.005 440 Dihedral : 12.788 81.499 896 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % 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: -2.83 (0.39), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS A 50 PHE 0.006 0.002 PHE D 94 TYR 0.003 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.293 Fit side-chains REVERT: A 94 PHE cc_start: 0.7566 (p90) cc_final: 0.7054 (p90) REVERT: B 46 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7513 (mt-10) REVERT: C 38 LEU cc_start: 0.8809 (tp) cc_final: 0.8583 (tm) REVERT: C 46 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7327 (mt-10) REVERT: C 94 PHE cc_start: 0.7546 (p90) cc_final: 0.6798 (p90) REVERT: D 94 PHE cc_start: 0.7724 (p90) cc_final: 0.7503 (p90) REVERT: E 38 LEU cc_start: 0.8894 (tp) cc_final: 0.8670 (tm) REVERT: E 94 PHE cc_start: 0.7910 (p90) cc_final: 0.7489 (p90) REVERT: F 94 PHE cc_start: 0.7880 (p90) cc_final: 0.7603 (p90) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 1.3687 time to fit residues: 100.4353 Evaluate side-chains 59 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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: 0.8432 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2640 Z= 0.130 Angle : 0.707 11.297 3580 Z= 0.320 Chirality : 0.053 0.128 462 Planarity : 0.003 0.019 440 Dihedral : 6.139 55.333 398 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.14 % Allowed : 13.26 % Favored : 85.61 % 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: -2.50 (0.41), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.89 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 50 PHE 0.008 0.002 PHE F 94 TYR 0.009 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 94 PHE cc_start: 0.7569 (p90) cc_final: 0.7067 (p90) REVERT: B 46 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7432 (mt-10) REVERT: C 94 PHE cc_start: 0.7574 (p90) cc_final: 0.6846 (p90) REVERT: D 44 THR cc_start: 0.8403 (m) cc_final: 0.8071 (p) REVERT: D 94 PHE cc_start: 0.7648 (p90) cc_final: 0.7177 (p90) REVERT: E 38 LEU cc_start: 0.8870 (tp) cc_final: 0.8641 (tm) REVERT: E 44 THR cc_start: 0.8496 (m) cc_final: 0.8078 (p) REVERT: E 94 PHE cc_start: 0.7964 (p90) cc_final: 0.7517 (p90) REVERT: F 44 THR cc_start: 0.8541 (m) cc_final: 0.8020 (p) outliers start: 3 outliers final: 0 residues processed: 64 average time/residue: 1.0672 time to fit residues: 70.0401 Evaluate side-chains 63 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 9 optimal weight: 0.0030 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 24 optimal weight: 8.9990 overall best weight: 1.3796 ------------------------------------------------------------------------------- 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: 0.8414 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2640 Z= 0.103 Angle : 0.644 9.844 3580 Z= 0.288 Chirality : 0.052 0.125 462 Planarity : 0.002 0.014 440 Dihedral : 5.068 39.595 398 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.14 % Allowed : 15.15 % Favored : 83.71 % 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: -2.28 (0.42), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 50 PHE 0.007 0.002 PHE F 94 TYR 0.007 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 0.303 Fit side-chains revert: symmetry clash REVERT: A 94 PHE cc_start: 0.7575 (p90) cc_final: 0.7087 (p90) REVERT: B 46 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7413 (mt-10) REVERT: B 94 PHE cc_start: 0.7437 (p90) cc_final: 0.7218 (p90) REVERT: C 94 PHE cc_start: 0.7561 (p90) cc_final: 0.6866 (p90) REVERT: D 44 THR cc_start: 0.8389 (m) cc_final: 0.8068 (p) REVERT: D 94 PHE cc_start: 0.7601 (p90) cc_final: 0.7139 (p90) REVERT: E 38 LEU cc_start: 0.8900 (tp) cc_final: 0.8661 (tm) REVERT: E 94 PHE cc_start: 0.7933 (p90) cc_final: 0.7520 (p90) REVERT: F 44 THR cc_start: 0.8621 (m) cc_final: 0.8186 (p) outliers start: 3 outliers final: 1 residues processed: 62 average time/residue: 1.0091 time to fit residues: 64.3031 Evaluate side-chains 62 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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: 0.8418 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2640 Z= 0.108 Angle : 0.647 9.720 3580 Z= 0.289 Chirality : 0.052 0.125 462 Planarity : 0.002 0.014 440 Dihedral : 4.863 41.166 398 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.76 % Allowed : 17.05 % Favored : 82.20 % 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: -2.19 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 50 PHE 0.009 0.002 PHE F 94 TYR 0.004 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 94 PHE cc_start: 0.7589 (p90) cc_final: 0.7120 (p90) REVERT: B 38 LEU cc_start: 0.8860 (tp) cc_final: 0.8596 (tp) REVERT: B 46 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7418 (mt-10) REVERT: B 94 PHE cc_start: 0.7461 (p90) cc_final: 0.7143 (p90) REVERT: C 94 PHE cc_start: 0.7614 (p90) cc_final: 0.6985 (p90) REVERT: D 44 THR cc_start: 0.8387 (m) cc_final: 0.8094 (p) REVERT: D 94 PHE cc_start: 0.7601 (p90) cc_final: 0.7149 (p90) REVERT: E 38 LEU cc_start: 0.8909 (tp) cc_final: 0.8656 (tm) REVERT: E 44 THR cc_start: 0.8303 (m) cc_final: 0.7978 (p) REVERT: E 94 PHE cc_start: 0.7847 (p90) cc_final: 0.7447 (p90) REVERT: F 44 THR cc_start: 0.8574 (m) cc_final: 0.8117 (p) outliers start: 2 outliers final: 0 residues processed: 60 average time/residue: 0.9126 time to fit residues: 56.3885 Evaluate side-chains 58 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 0.0370 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 2640 Z= 0.158 Angle : 0.714 11.142 3580 Z= 0.323 Chirality : 0.054 0.130 462 Planarity : 0.002 0.012 440 Dihedral : 5.177 44.650 398 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 1.14 % Allowed : 16.29 % Favored : 82.58 % 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: -2.26 (0.42), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 PHE 0.010 0.002 PHE F 94 TYR 0.005 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 94 PHE cc_start: 0.7574 (p90) cc_final: 0.7088 (p90) REVERT: B 46 GLU cc_start: 0.7652 (mt-10) cc_final: 0.7399 (mt-10) REVERT: C 94 PHE cc_start: 0.7562 (p90) cc_final: 0.6918 (p90) REVERT: D 44 THR cc_start: 0.8453 (m) cc_final: 0.8108 (p) REVERT: D 94 PHE cc_start: 0.7655 (p90) cc_final: 0.7211 (p90) REVERT: E 38 LEU cc_start: 0.8891 (tp) cc_final: 0.8654 (tm) REVERT: E 44 THR cc_start: 0.8353 (m) cc_final: 0.7956 (p) REVERT: E 94 PHE cc_start: 0.7923 (p90) cc_final: 0.7570 (p90) REVERT: F 44 THR cc_start: 0.8558 (m) cc_final: 0.8088 (p) outliers start: 3 outliers final: 1 residues processed: 62 average time/residue: 1.1190 time to fit residues: 71.1679 Evaluate side-chains 61 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 2 optimal weight: 6.9990 chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2640 Z= 0.126 Angle : 0.677 10.579 3580 Z= 0.303 Chirality : 0.053 0.128 462 Planarity : 0.002 0.012 440 Dihedral : 4.911 43.864 398 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.00 % Allowed : 17.80 % Favored : 82.20 % 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: -2.19 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.66 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 50 PHE 0.009 0.002 PHE F 94 TYR 0.004 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.299 Fit side-chains revert: symmetry clash REVERT: A 94 PHE cc_start: 0.7565 (p90) cc_final: 0.7092 (p90) REVERT: B 46 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7423 (mt-10) REVERT: B 94 PHE cc_start: 0.7551 (p90) cc_final: 0.7266 (p90) REVERT: C 94 PHE cc_start: 0.7551 (p90) cc_final: 0.6912 (p90) REVERT: D 44 THR cc_start: 0.8432 (m) cc_final: 0.8085 (p) REVERT: D 94 PHE cc_start: 0.7632 (p90) cc_final: 0.7187 (p90) REVERT: E 38 LEU cc_start: 0.8857 (tp) cc_final: 0.8629 (tm) REVERT: E 44 THR cc_start: 0.8320 (m) cc_final: 0.7986 (p) REVERT: E 94 PHE cc_start: 0.7883 (p90) cc_final: 0.7527 (p90) REVERT: F 44 THR cc_start: 0.8554 (m) cc_final: 0.8098 (p) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.9429 time to fit residues: 56.3260 Evaluate side-chains 58 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 0.0670 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 0.0470 chunk 16 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 5.9990 overall best weight: 1.4220 ------------------------------------------------------------------------------- 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: 0.8410 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2640 Z= 0.103 Angle : 0.643 9.652 3580 Z= 0.284 Chirality : 0.052 0.125 462 Planarity : 0.002 0.011 440 Dihedral : 4.704 42.953 398 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 17.80 % Favored : 82.20 % 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: -2.09 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.58 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS A 50 PHE 0.009 0.002 PHE F 94 TYR 0.004 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 94 PHE cc_start: 0.7557 (p90) cc_final: 0.7090 (p90) REVERT: B 46 GLU cc_start: 0.7645 (mt-10) cc_final: 0.7423 (mt-10) REVERT: B 94 PHE cc_start: 0.7561 (p90) cc_final: 0.7259 (p90) REVERT: C 94 PHE cc_start: 0.7548 (p90) cc_final: 0.6904 (p90) REVERT: D 44 THR cc_start: 0.8400 (m) cc_final: 0.8082 (p) REVERT: D 94 PHE cc_start: 0.7627 (p90) cc_final: 0.7181 (p90) REVERT: E 38 LEU cc_start: 0.8863 (tp) cc_final: 0.8644 (tm) REVERT: E 44 THR cc_start: 0.8319 (m) cc_final: 0.8005 (p) REVERT: E 94 PHE cc_start: 0.7814 (p90) cc_final: 0.7459 (p90) REVERT: F 44 THR cc_start: 0.8583 (m) cc_final: 0.8151 (p) outliers start: 0 outliers final: 1 residues processed: 63 average time/residue: 0.9947 time to fit residues: 64.4111 Evaluate side-chains 62 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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: 0.8455 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2640 Z= 0.230 Angle : 0.802 12.287 3580 Z= 0.372 Chirality : 0.057 0.136 462 Planarity : 0.002 0.010 440 Dihedral : 5.387 40.860 398 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.76 % Allowed : 17.05 % Favored : 82.20 % 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: -2.30 (0.42), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS F 50 PHE 0.011 0.002 PHE F 94 TYR 0.004 0.001 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 94 PHE cc_start: 0.7614 (p90) cc_final: 0.7118 (p90) REVERT: B 46 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7427 (mt-10) REVERT: C 94 PHE cc_start: 0.7524 (p90) cc_final: 0.6900 (p90) REVERT: D 94 PHE cc_start: 0.7663 (p90) cc_final: 0.7185 (p90) REVERT: E 38 LEU cc_start: 0.8919 (tp) cc_final: 0.8672 (tm) REVERT: E 44 THR cc_start: 0.8355 (m) cc_final: 0.7928 (p) REVERT: E 94 PHE cc_start: 0.7910 (p90) cc_final: 0.7539 (p90) REVERT: F 44 THR cc_start: 0.8511 (m) cc_final: 0.7985 (p) outliers start: 2 outliers final: 0 residues processed: 62 average time/residue: 1.0716 time to fit residues: 68.1484 Evaluate side-chains 62 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 28 optimal weight: 0.0050 overall best weight: 1.5800 ------------------------------------------------------------------------------- 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: 0.8418 moved from start: 0.2035 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= 0.116 Angle : 0.687 10.611 3580 Z= 0.304 Chirality : 0.053 0.125 462 Planarity : 0.002 0.013 440 Dihedral : 4.792 44.291 398 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 18.18 % Favored : 81.82 % 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: -2.14 (0.43), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.62 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.009 0.002 PHE F 94 TYR 0.005 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 60 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 94 PHE cc_start: 0.7537 (p90) cc_final: 0.7052 (p90) REVERT: B 46 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7418 (mt-10) REVERT: B 94 PHE cc_start: 0.7472 (p90) cc_final: 0.7254 (p90) REVERT: C 94 PHE cc_start: 0.7508 (p90) cc_final: 0.7033 (p90) REVERT: D 44 THR cc_start: 0.8417 (m) cc_final: 0.8085 (p) REVERT: D 94 PHE cc_start: 0.7618 (p90) cc_final: 0.7167 (p90) REVERT: E 38 LEU cc_start: 0.8867 (tp) cc_final: 0.8650 (tm) REVERT: E 44 THR cc_start: 0.8364 (m) cc_final: 0.8033 (p) REVERT: F 44 THR cc_start: 0.8572 (m) cc_final: 0.8143 (p) outliers start: 0 outliers final: 1 residues processed: 60 average time/residue: 1.0887 time to fit residues: 67.0252 Evaluate side-chains 61 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.8445 moved from start: 0.1970 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= 0.192 Angle : 0.781 11.686 3580 Z= 0.360 Chirality : 0.055 0.132 462 Planarity : 0.002 0.016 440 Dihedral : 5.237 43.323 398 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.38 % Allowed : 17.80 % Favored : 81.82 % 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: -2.27 (0.42), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.72 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS E 50 PHE 0.011 0.002 PHE F 94 TYR 0.004 0.001 TYR A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.276 Fit side-chains revert: symmetry clash REVERT: A 94 PHE cc_start: 0.7550 (p90) cc_final: 0.7114 (p90) REVERT: B 46 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7432 (mt-10) REVERT: B 94 PHE cc_start: 0.7514 (p90) cc_final: 0.7247 (p90) REVERT: C 94 PHE cc_start: 0.7488 (p90) cc_final: 0.7076 (p90) REVERT: D 94 PHE cc_start: 0.7650 (p90) cc_final: 0.7179 (p90) REVERT: E 38 LEU cc_start: 0.8898 (tp) cc_final: 0.8667 (tm) REVERT: E 44 THR cc_start: 0.8377 (m) cc_final: 0.7971 (p) REVERT: F 44 THR cc_start: 0.8510 (m) cc_final: 0.8005 (p) outliers start: 1 outliers final: 0 residues processed: 62 average time/residue: 1.0632 time to fit residues: 67.6826 Evaluate side-chains 62 residues out of total 252 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.149044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.115016 restraints weight = 12091.742| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 3.53 r_work: 0.3586 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3584 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3584 r_free = 0.3584 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3583 r_free = 0.3583 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2640 Z= 0.170 Angle : 0.764 11.565 3580 Z= 0.348 Chirality : 0.054 0.131 462 Planarity : 0.002 0.016 440 Dihedral : 5.124 43.833 398 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.38 % Allowed : 17.80 % Favored : 81.82 % 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: -2.25 (0.42), residues: 372 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS E 50 PHE 0.011 0.002 PHE E 94 TYR 0.004 0.001 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1812.96 seconds wall clock time: 33 minutes 8.39 seconds (1988.39 seconds total)