Starting phenix.real_space_refine (version: dev) on Fri Feb 17 06:00:54 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvk_32099/02_2023/8gvk_32099.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvk_32099/02_2023/8gvk_32099.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvk_32099/02_2023/8gvk_32099.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvk_32099/02_2023/8gvk_32099.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvk_32099/02_2023/8gvk_32099.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gvk_32099/02_2023/8gvk_32099.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.004 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 Process input model Symmetric amino acids flipped Residue "B ARG 53": "NH1" <-> "NH2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 3567 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 887 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 2.42, per 1000 atoms: 0.68 Number of scatterers: 3567 At special positions: 0 Unit cell: (68.0021, 57.6201, 62.8111, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 723 8.00 N 620 7.00 C 2224 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: 1.30 Conformation dependent library (CDL) restraints added in 495.0 milliseconds 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 3.4% alpha, 52.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'D' and resid 118 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 23 removed outlier: 5.335A pdb=" N VAL A 55 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA A 78 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER A 88 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 19 through 23 removed outlier: 5.334A pdb=" N VAL B 55 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA B 78 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N SER B 88 " --> pdb=" O TRP B 79 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 19 through 23 removed outlier: 5.335A pdb=" N VAL C 55 " --> pdb=" O ALA C 78 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA C 78 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER C 88 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 19 through 23 removed outlier: 5.335A pdb=" N VAL D 55 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA D 78 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N SER D 88 " --> pdb=" O TRP D 79 " (cutoff:3.500A) 192 hydrogen bonds defined for protein. 516 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: 0.94 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 572 1.29 - 1.37: 640 1.37 - 1.44: 524 1.44 - 1.51: 770 1.51 - 1.58: 1130 Bond restraints: 3636 Sorted by residual: bond pdb=" N ARG B 53 " pdb=" CA ARG B 53 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.22e-02 6.72e+03 5.95e+00 bond pdb=" N ARG C 53 " pdb=" CA ARG C 53 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.22e-02 6.72e+03 5.95e+00 bond pdb=" N ARG A 53 " pdb=" CA ARG A 53 " ideal model delta sigma weight residual 1.455 1.485 -0.029 1.22e-02 6.72e+03 5.79e+00 bond pdb=" N ARG D 53 " pdb=" CA ARG D 53 " ideal model delta sigma weight residual 1.455 1.485 -0.029 1.22e-02 6.72e+03 5.75e+00 bond pdb=" CB GLU D 101 " pdb=" CG GLU D 101 " ideal model delta sigma weight residual 1.520 1.584 -0.064 3.00e-02 1.11e+03 4.56e+00 ... (remaining 3631 not shown) Histogram of bond angle deviations from ideal: 102.98 - 109.19: 459 109.19 - 115.41: 1808 115.41 - 121.62: 1650 121.62 - 127.84: 995 127.84 - 134.05: 64 Bond angle restraints: 4976 Sorted by residual: angle pdb=" CA GLU A 101 " pdb=" CB GLU A 101 " pdb=" CG GLU A 101 " ideal model delta sigma weight residual 114.10 125.96 -11.86 2.00e+00 2.50e-01 3.52e+01 angle pdb=" CA GLU C 101 " pdb=" CB GLU C 101 " pdb=" CG GLU C 101 " ideal model delta sigma weight residual 114.10 125.94 -11.84 2.00e+00 2.50e-01 3.50e+01 angle pdb=" CA GLU B 101 " pdb=" CB GLU B 101 " pdb=" CG GLU B 101 " ideal model delta sigma weight residual 114.10 125.94 -11.84 2.00e+00 2.50e-01 3.50e+01 angle pdb=" CA GLU D 101 " pdb=" CB GLU D 101 " pdb=" CG GLU D 101 " ideal model delta sigma weight residual 114.10 125.90 -11.80 2.00e+00 2.50e-01 3.48e+01 angle pdb=" C ALA A 46 " pdb=" N VAL A 47 " pdb=" CA VAL A 47 " ideal model delta sigma weight residual 121.97 131.28 -9.31 1.80e+00 3.09e-01 2.68e+01 ... (remaining 4971 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 1776 16.70 - 33.41: 148 33.41 - 50.11: 44 50.11 - 66.82: 8 66.82 - 83.52: 8 Dihedral angle restraints: 1984 sinusoidal: 664 harmonic: 1320 Sorted by residual: dihedral pdb=" CA ALA C 46 " pdb=" C ALA C 46 " pdb=" N VAL C 47 " pdb=" CA VAL C 47 " ideal model delta harmonic sigma weight residual 180.00 -103.09 -76.91 0 5.00e+00 4.00e-02 2.37e+02 dihedral pdb=" CA ALA B 46 " pdb=" C ALA B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta harmonic sigma weight residual 180.00 -103.12 -76.88 0 5.00e+00 4.00e-02 2.36e+02 dihedral pdb=" CA ALA A 46 " pdb=" C ALA A 46 " pdb=" N VAL A 47 " pdb=" CA VAL A 47 " ideal model delta harmonic sigma weight residual -180.00 -103.15 -76.85 0 5.00e+00 4.00e-02 2.36e+02 ... (remaining 1981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 340 0.046 - 0.093: 159 0.093 - 0.139: 41 0.139 - 0.185: 8 0.185 - 0.231: 8 Chirality restraints: 556 Sorted by residual: chirality pdb=" CB ILE B 17 " pdb=" CA ILE B 17 " pdb=" CG1 ILE B 17 " pdb=" CG2 ILE B 17 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB ILE D 17 " pdb=" CA ILE D 17 " pdb=" CG1 ILE D 17 " pdb=" CG2 ILE D 17 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CB ILE A 17 " pdb=" CA ILE A 17 " pdb=" CG1 ILE A 17 " pdb=" CG2 ILE A 17 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.31e+00 ... (remaining 553 not shown) Planarity restraints: 624 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 101 " -0.013 2.00e-02 2.50e+03 2.58e-02 6.64e+00 pdb=" C GLU B 101 " 0.045 2.00e-02 2.50e+03 pdb=" O GLU B 101 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA B 102 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 101 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.60e+00 pdb=" C GLU D 101 " -0.044 2.00e-02 2.50e+03 pdb=" O GLU D 101 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA D 102 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 101 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.54e+00 pdb=" C GLU A 101 " -0.044 2.00e-02 2.50e+03 pdb=" O GLU A 101 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA A 102 " 0.015 2.00e-02 2.50e+03 ... (remaining 621 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 76 2.63 - 3.19: 2732 3.19 - 3.76: 6021 3.76 - 4.33: 8262 4.33 - 4.90: 13553 Nonbonded interactions: 30644 Sorted by model distance: nonbonded pdb=" O SER D 69 " pdb=" O HOH D 201 " model vdw 2.057 2.440 nonbonded pdb=" O SER B 69 " pdb=" O HOH B 201 " model vdw 2.178 2.440 nonbonded pdb=" O SER A 69 " pdb=" O HOH A 201 " model vdw 2.219 2.440 nonbonded pdb=" OE2 GLU B 44 " pdb=" NH1 ARG B 53 " model vdw 2.228 2.520 nonbonded pdb=" O SER C 69 " pdb=" O HOH C 201 " model vdw 2.251 2.440 ... (remaining 30639 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 2224 2.51 5 N 620 2.21 5 O 723 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.960 Check model and map are aligned: 0.060 Process input model: 14.140 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 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 : 0.006 0.064 3636 Z= 0.424 Angle : 1.289 11.858 4976 Z= 0.716 Chirality : 0.059 0.231 556 Planarity : 0.005 0.026 624 Dihedral : 15.347 83.520 1160 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 2.56 % Allowed : 3.42 % Favored : 94.02 % Rotamer Outliers : 4.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 2.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.33), residues: 468 helix: None (None), residues: 0 sheet: -0.66 (0.27), residues: 264 loop : -1.39 (0.36), residues: 204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.428 Fit side-chains outliers start: 14 outliers final: 0 residues processed: 71 average time/residue: 1.3553 time to fit residues: 99.0315 Evaluate side-chains 43 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 11 optimal weight: 20.0000 chunk 22 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 ASN B 107 GLN B 118 ASN B 127 HIS C 107 GLN C 118 ASN C 127 HIS D 118 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3636 Z= 0.268 Angle : 0.861 7.108 4976 Z= 0.463 Chirality : 0.048 0.170 556 Planarity : 0.004 0.028 624 Dihedral : 8.987 61.115 512 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 2.35 % Allowed : 4.27 % Favored : 93.38 % Rotamer Outliers : 6.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.71 % 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: -0.64 (0.34), residues: 468 helix: None (None), residues: 0 sheet: -0.09 (0.26), residues: 288 loop : -0.81 (0.43), residues: 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 50 time to evaluate : 0.419 Fit side-chains outliers start: 23 outliers final: 10 residues processed: 66 average time/residue: 1.3546 time to fit residues: 91.8889 Evaluate side-chains 54 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 1 average time/residue: 0.0357 time to fit residues: 0.5678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 33 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 43 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 20.0000 chunk 32 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN D 107 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 3636 Z= 0.355 Angle : 0.918 7.585 4976 Z= 0.490 Chirality : 0.051 0.188 556 Planarity : 0.005 0.038 624 Dihedral : 8.827 56.804 512 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.70 % Favored : 94.44 % Rotamer Outliers : 4.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.33), residues: 468 helix: -4.50 (0.35), residues: 24 sheet: 0.31 (0.26), residues: 284 loop : -2.00 (0.41), residues: 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 48 time to evaluate : 0.398 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 62 average time/residue: 1.2562 time to fit residues: 80.2880 Evaluate side-chains 53 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 1 average time/residue: 0.0366 time to fit residues: 0.6111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 107 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 3636 Z= 0.197 Angle : 0.761 6.743 4976 Z= 0.402 Chirality : 0.045 0.175 556 Planarity : 0.004 0.027 624 Dihedral : 7.865 50.322 512 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.85 % Allowed : 3.85 % Favored : 95.30 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.34), residues: 468 helix: -4.65 (0.30), residues: 24 sheet: 0.46 (0.26), residues: 288 loop : -1.69 (0.44), residues: 156 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.414 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 63 average time/residue: 1.2395 time to fit residues: 80.5898 Evaluate side-chains 50 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 45 time to evaluate : 0.396 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.5078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 31 optimal weight: 20.0000 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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: 0.8063 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 3636 Z= 0.247 Angle : 0.776 7.499 4976 Z= 0.417 Chirality : 0.046 0.171 556 Planarity : 0.004 0.032 624 Dihedral : 7.783 46.262 512 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.91 % Favored : 94.23 % Rotamer Outliers : 4.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % 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: -0.93 (0.34), residues: 468 helix: -4.46 (0.36), residues: 24 sheet: 0.33 (0.25), residues: 288 loop : -1.72 (0.44), residues: 156 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 44 time to evaluate : 0.376 Fit side-chains outliers start: 15 outliers final: 10 residues processed: 58 average time/residue: 1.3039 time to fit residues: 78.0038 Evaluate side-chains 54 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.432 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 0.5711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 3 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 22 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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: 0.8068 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 3636 Z= 0.285 Angle : 0.800 7.562 4976 Z= 0.429 Chirality : 0.047 0.161 556 Planarity : 0.004 0.034 624 Dihedral : 7.570 39.612 512 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 1.71 % Allowed : 4.27 % Favored : 94.02 % Rotamer Outliers : 3.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.85 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.34), residues: 468 helix: -4.46 (0.35), residues: 24 sheet: 0.32 (0.25), residues: 288 loop : -1.78 (0.45), residues: 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.383 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 55 average time/residue: 1.3137 time to fit residues: 74.4238 Evaluate side-chains 53 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 0.4833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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: 0.8071 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 3636 Z= 0.294 Angle : 0.802 7.584 4976 Z= 0.429 Chirality : 0.048 0.163 556 Planarity : 0.005 0.036 624 Dihedral : 7.230 27.421 512 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.13 % Favored : 94.02 % Rotamer Outliers : 4.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.33), residues: 468 helix: -4.31 (0.42), residues: 24 sheet: 0.29 (0.25), residues: 288 loop : -1.89 (0.43), residues: 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 44 time to evaluate : 0.378 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 56 average time/residue: 1.3643 time to fit residues: 78.7063 Evaluate side-chains 53 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.361 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 0.4833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 9.9990 chunk 3 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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: 0.8068 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 3636 Z= 0.254 Angle : 0.774 7.295 4976 Z= 0.414 Chirality : 0.047 0.148 556 Planarity : 0.005 0.043 624 Dihedral : 7.059 25.793 512 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.13 % Favored : 94.02 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.34), residues: 468 helix: -4.33 (0.41), residues: 24 sheet: 0.12 (0.25), residues: 296 loop : -1.67 (0.46), residues: 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.383 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 53 average time/residue: 1.4106 time to fit residues: 76.9106 Evaluate side-chains 53 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 0.5200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 29 optimal weight: 30.0000 chunk 43 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 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: 0.8069 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 3636 Z= 0.274 Angle : 0.791 7.430 4976 Z= 0.422 Chirality : 0.047 0.145 556 Planarity : 0.005 0.043 624 Dihedral : 7.149 24.446 512 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.85 % Allowed : 5.13 % Favored : 94.02 % Rotamer Outliers : 2.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.34), residues: 468 helix: -4.28 (0.43), residues: 24 sheet: 0.12 (0.25), residues: 296 loop : -1.71 (0.45), residues: 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.414 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 54 average time/residue: 1.3985 time to fit residues: 77.6449 Evaluate side-chains 53 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 44 time to evaluate : 0.378 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 0.4968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 34 optimal weight: 8.9990 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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: 0.8062 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 3636 Z= 0.226 Angle : 0.757 7.071 4976 Z= 0.403 Chirality : 0.045 0.137 556 Planarity : 0.005 0.047 624 Dihedral : 6.967 26.015 512 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.70 % Favored : 94.44 % Rotamer Outliers : 3.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.34), residues: 468 helix: -4.37 (0.40), residues: 24 sheet: 0.15 (0.26), residues: 296 loop : -1.62 (0.47), residues: 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 936 Ramachandran restraints generated. 468 Oldfield, 0 Emsley, 468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 41 time to evaluate : 0.413 Fit side-chains outliers start: 11 outliers final: 9 residues processed: 52 average time/residue: 1.4012 time to fit residues: 75.0378 Evaluate side-chains 50 residues out of total 352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 41 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 9 residues processed: 0 time to fit residues: 0.4602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 8.9990 chunk 6 optimal weight: 3.9990 chunk 30 optimal weight: 0.9990 chunk 1 optimal weight: 0.0370 chunk 25 optimal weight: 9.9990 chunk 40 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.8064 ------------------------------------------------------------------------------- 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 = 0.3980 r_free = 0.3980 target = 0.171872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.140869 restraints weight = 2978.731| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 1.41 r_work: 0.3474 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 3636 Z= 0.168 Angle : 0.702 6.468 4976 Z= 0.376 Chirality : 0.043 0.136 556 Planarity : 0.004 0.045 624 Dihedral : 6.614 27.402 512 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.85 % Allowed : 4.27 % Favored : 94.87 % Rotamer Outliers : 2.62 % 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: -0.94 (0.35), residues: 468 helix: -4.61 (0.30), residues: 24 sheet: 0.20 (0.26), residues: 296 loop : -1.49 (0.48), residues: 148 =============================================================================== Job complete usr+sys time: 1758.27 seconds wall clock time: 32 minutes 4.14 seconds (1924.14 seconds total)