Mon 24 Dec 07:33:24 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2prr-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2prr-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2prr-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-4.0-parrot-noncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-4.0-parrot-noncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Mon 24 Dec 07:33:28 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2prr-4.0-parrot-noncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 1687 and 0 Target number of residues in the AU: 1687 Target solvent content: 0.6799 Checking the provided sequence file Detected sequence length: 197 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 12 Adjusted target number of residues: 2364 Adjusted target solvent content: 0.55 Input MTZ file: 2prr-4.0-parrot-noncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 1 Cell parameters: 65.105 93.953 120.898 84.262 81.638 77.734 Input sequence file: 2prr-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 18912 target number of atoms Had to go as low as 0.80 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 119.307 4.000 Wilson plot Bfac: 101.00 Failed to save intermediate PDB 22829 reflections ( 97.72 % complete ) and 0 restraints for refining 20939 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3307 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2961 (Rfree = 0.000) for 20939 atoms. Found 99 (99 requested) and removed 384 (49 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.98 3.72 Search for helices and strands: 0 residues in 0 chains, 21103 seeds are put forward NCS extension: 0 residues added, 21103 seeds are put forward Round 1: 764 peptides, 156 chains. Longest chain 9 peptides. Score 0.267 Round 2: 987 peptides, 165 chains. Longest chain 16 peptides. Score 0.383 Round 3: 1030 peptides, 161 chains. Longest chain 19 peptides. Score 0.418 Round 4: 1047 peptides, 160 chains. Longest chain 22 peptides. Score 0.430 Round 5: 1087 peptides, 162 chains. Longest chain 25 peptides. Score 0.447 Taking the results from Round 5 Chains 163, Residues 925, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 40689 restraints for refining 17074 atoms. 37060 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2250 (Rfree = 0.000) for 17074 atoms. Found 30 (81 requested) and removed 116 (40 requested) atoms. Cycle 2: After refmac, R = 0.2113 (Rfree = 0.000) for 16738 atoms. Found 43 (80 requested) and removed 102 (40 requested) atoms. Failed to save intermediate PDB Cycle 3: After refmac, R = 0.1962 (Rfree = 0.000) for 16518 atoms. Found 37 (79 requested) and removed 83 (39 requested) atoms. Cycle 4: After refmac, R = 0.1988 (Rfree = 0.000) for 16383 atoms. Found 51 (78 requested) and removed 87 (39 requested) atoms. Cycle 5: After refmac, R = 0.1911 (Rfree = 0.000) for 16272 atoms. Found 47 (77 requested) and removed 85 (38 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.90 3.65 Search for helices and strands: 0 residues in 0 chains, 16930 seeds are put forward NCS extension: 25 residues added (0 deleted due to clashes), 16955 seeds are put forward Round 1: 931 peptides, 177 chains. Longest chain 18 peptides. Score 0.318 Round 2: 1097 peptides, 169 chains. Longest chain 19 peptides. Score 0.435 Round 3: 1155 peptides, 170 chains. Longest chain 21 peptides. Score 0.464 Round 4: 1147 peptides, 170 chains. Longest chain 27 peptides. Score 0.460 Round 5: 1151 peptides, 161 chains. Longest chain 21 peptides. Score 0.483 Taking the results from Round 5 Chains 161, Residues 990, Estimated correctness of the model 0.0 % 3 chains (14 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 40158 restraints for refining 17072 atoms. 36319 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.1980 (Rfree = 0.000) for 17072 atoms. Found 39 (81 requested) and removed 150 (40 requested) atoms. Failed to save intermediate PDB Cycle 7: After refmac, R = 0.1941 (Rfree = 0.000) for 16825 atoms. Found 50 (80 requested) and removed 110 (40 requested) atoms. Cycle 8: After refmac, R = 0.1869 (Rfree = 0.000) for 16671 atoms. Found 57 (79 requested) and removed 92 (39 requested) atoms. Cycle 9: After refmac, R = 0.1792 (Rfree = 0.000) for 16567 atoms. Found 58 (79 requested) and removed 80 (39 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1737 (Rfree = 0.000) for 16498 atoms. Found 46 (78 requested) and removed 74 (39 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.90 3.65 Search for helices and strands: 0 residues in 0 chains, 17212 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 17225 seeds are put forward Round 1: 962 peptides, 181 chains. Longest chain 15 peptides. Score 0.326 Round 2: 1047 peptides, 166 chains. Longest chain 18 peptides. Score 0.415 Round 3: 1072 peptides, 164 chains. Longest chain 17 peptides. Score 0.434 Round 4: 1076 peptides, 163 chains. Longest chain 18 peptides. Score 0.438 Round 5: 1095 peptides, 150 chains. Longest chain 28 peptides. Score 0.480 Taking the results from Round 5 Chains 154, Residues 945, Estimated correctness of the model 0.0 % 6 chains (54 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 39377 restraints for refining 17075 atoms. 35547 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1816 (Rfree = 0.000) for 17075 atoms. Found 35 (81 requested) and removed 74 (40 requested) atoms. Cycle 12: After refmac, R = 0.1797 (Rfree = 0.000) for 16906 atoms. Found 42 (80 requested) and removed 75 (40 requested) atoms. Cycle 13: After refmac, R = 0.1748 (Rfree = 0.000) for 16807 atoms. Found 44 (80 requested) and removed 66 (40 requested) atoms. Cycle 14: After refmac, R = 0.1738 (Rfree = 0.000) for 16721 atoms. Found 50 (79 requested) and removed 73 (39 requested) atoms. Cycle 15: After refmac, R = 0.1675 (Rfree = 0.000) for 16656 atoms. Found 47 (79 requested) and removed 62 (39 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.92 3.67 Search for helices and strands: 0 residues in 0 chains, 17286 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 17309 seeds are put forward Round 1: 958 peptides, 179 chains. Longest chain 18 peptides. Score 0.329 Round 2: 1076 peptides, 168 chains. Longest chain 21 peptides. Score 0.426 Round 3: 1107 peptides, 165 chains. Longest chain 18 peptides. Score 0.450 Round 4: 1112 peptides, 162 chains. Longest chain 20 peptides. Score 0.460 Round 5: 1112 peptides, 155 chains. Longest chain 19 peptides. Score 0.477 Taking the results from Round 5 Chains 158, Residues 957, Estimated correctness of the model 0.0 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 39072 restraints for refining 17075 atoms. 35223 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1834 (Rfree = 0.000) for 17075 atoms. Found 36 (81 requested) and removed 98 (40 requested) atoms. Cycle 17: After refmac, R = 0.1784 (Rfree = 0.000) for 16903 atoms. Found 50 (80 requested) and removed 79 (40 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.1742 (Rfree = 0.000) for 16811 atoms. Found 48 (80 requested) and removed 68 (40 requested) atoms. Cycle 19: After refmac, R = 0.1621 (Rfree = 0.000) for 16748 atoms. Found 39 (79 requested) and removed 70 (39 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1293 (Rfree = 0.000) for 16682 atoms. Found 8 (79 requested) and removed 53 (39 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.91 3.66 Search for helices and strands: 0 residues in 0 chains, 17169 seeds are put forward NCS extension: 21 residues added (1 deleted due to clashes), 17190 seeds are put forward Round 1: 963 peptides, 183 chains. Longest chain 15 peptides. Score 0.322 Round 2: 1035 peptides, 166 chains. Longest chain 18 peptides. Score 0.408 Round 3: 1032 peptides, 158 chains. Longest chain 18 peptides. Score 0.426 Round 4: 1031 peptides, 155 chains. Longest chain 18 peptides. Score 0.433 Round 5: 1046 peptides, 152 chains. Longest chain 18 peptides. Score 0.449 Taking the results from Round 5 Chains 153, Residues 894, Estimated correctness of the model 0.0 % 3 chains (24 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 39751 restraints for refining 17078 atoms. 36230 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1783 (Rfree = 0.000) for 17078 atoms. Found 33 (81 requested) and removed 82 (40 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1782 (Rfree = 0.000) for 16936 atoms. Found 56 (80 requested) and removed 71 (40 requested) atoms. Cycle 23: After refmac, R = 0.1740 (Rfree = 0.000) for 16858 atoms. Found 55 (80 requested) and removed 79 (40 requested) atoms. Cycle 24: After refmac, R = 0.1652 (Rfree = 0.000) for 16799 atoms. Found 57 (79 requested) and removed 65 (39 requested) atoms. Cycle 25: After refmac, R = 0.1275 (Rfree = 0.000) for 16765 atoms. Found 9 (79 requested) and removed 47 (39 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.91 3.66 Search for helices and strands: 0 residues in 0 chains, 17299 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 17322 seeds are put forward Round 1: 881 peptides, 173 chains. Longest chain 17 peptides. Score 0.297 Round 2: 984 peptides, 166 chains. Longest chain 16 peptides. Score 0.379 Round 3: 1018 peptides, 165 chains. Longest chain 19 peptides. Score 0.401 Round 4: 1043 peptides, 164 chains. Longest chain 17 peptides. Score 0.418 Round 5: 997 peptides, 158 chains. Longest chain 15 peptides. Score 0.407 Taking the results from Round 4 Chains 164, Residues 879, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 40160 restraints for refining 17078 atoms. 36763 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1779 (Rfree = 0.000) for 17078 atoms. Found 42 (81 requested) and removed 75 (40 requested) atoms. Cycle 27: After refmac, R = 0.1836 (Rfree = 0.000) for 16964 atoms. Found 77 (80 requested) and removed 79 (40 requested) atoms. Cycle 28: After refmac, R = 0.1705 (Rfree = 0.000) for 16899 atoms. Found 71 (80 requested) and removed 71 (40 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.1650 (Rfree = 0.000) for 16862 atoms. Found 69 (80 requested) and removed 72 (40 requested) atoms. Cycle 30: After refmac, R = 0.1234 (Rfree = 0.000) for 16826 atoms. Found 16 (80 requested) and removed 51 (40 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.91 3.66 Search for helices and strands: 0 residues in 0 chains, 17311 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 17325 seeds are put forward Round 1: 840 peptides, 174 chains. Longest chain 12 peptides. Score 0.267 Round 2: 926 peptides, 159 chains. Longest chain 14 peptides. Score 0.362 Round 3: 940 peptides, 156 chains. Longest chain 14 peptides. Score 0.379 Round 4: 929 peptides, 151 chains. Longest chain 16 peptides. Score 0.385 Round 5: 925 peptides, 149 chains. Longest chain 25 peptides. Score 0.388 Taking the results from Round 5 Chains 150, Residues 776, Estimated correctness of the model 0.0 % 2 chains (26 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 40193 restraints for refining 17077 atoms. 37128 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1706 (Rfree = 0.000) for 17077 atoms. Found 46 (81 requested) and removed 67 (40 requested) atoms. Cycle 32: After refmac, R = 0.1712 (Rfree = 0.000) for 16958 atoms. Found 68 (81 requested) and removed 73 (40 requested) atoms. Cycle 33: After refmac, R = 0.1691 (Rfree = 0.000) for 16917 atoms. Found 66 (80 requested) and removed 68 (40 requested) atoms. Cycle 34: After refmac, R = 0.1621 (Rfree = 0.000) for 16881 atoms. Found 69 (80 requested) and removed 74 (40 requested) atoms. Cycle 35: After refmac, R = 0.1228 (Rfree = 0.000) for 16850 atoms. Found 13 (80 requested) and removed 48 (40 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.93 3.68 Search for helices and strands: 0 residues in 0 chains, 17275 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 17299 seeds are put forward Round 1: 798 peptides, 169 chains. Longest chain 9 peptides. Score 0.253 Round 2: 890 peptides, 154 chains. Longest chain 13 peptides. Score 0.354 Round 3: 875 peptides, 151 chains. Longest chain 11 peptides. Score 0.353 Round 4: 909 peptides, 148 chains. Longest chain 18 peptides. Score 0.381 Round 5: 905 peptides, 155 chains. Longest chain 15 peptides. Score 0.360 Taking the results from Round 4 Chains 149, Residues 761, Estimated correctness of the model 0.0 % 3 chains (26 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 40288 restraints for refining 17074 atoms. 37309 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1744 (Rfree = 0.000) for 17074 atoms. Found 64 (81 requested) and removed 63 (40 requested) atoms. Cycle 37: After refmac, R = 0.1732 (Rfree = 0.000) for 17008 atoms. Found 75 (81 requested) and removed 70 (40 requested) atoms. Cycle 38: After refmac, R = 0.1695 (Rfree = 0.000) for 16964 atoms. Found 80 (80 requested) and removed 71 (40 requested) atoms. Cycle 39: After refmac, R = 0.1667 (Rfree = 0.000) for 16932 atoms. Found 75 (80 requested) and removed 64 (40 requested) atoms. Cycle 40: After refmac, R = 0.1660 (Rfree = 0.000) for 16894 atoms. Found 77 (80 requested) and removed 59 (40 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.92 3.67 Search for helices and strands: 0 residues in 0 chains, 17352 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 17364 seeds are put forward Round 1: 702 peptides, 149 chains. Longest chain 12 peptides. Score 0.245 Round 2: 815 peptides, 153 chains. Longest chain 11 peptides. Score 0.309 Round 3: 821 peptides, 148 chains. Longest chain 13 peptides. Score 0.327 Round 4: 809 peptides, 142 chains. Longest chain 18 peptides. Score 0.336 Round 5: 812 peptides, 142 chains. Longest chain 13 peptides. Score 0.338 Taking the results from Round 5 Chains 142, Residues 670, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 22829 reflections ( 97.72 % complete ) and 40791 restraints for refining 17075 atoms. 38128 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1819 (Rfree = 0.000) for 17075 atoms. Found 80 (81 requested) and removed 77 (40 requested) atoms. Failed to save intermediate PDB Cycle 42: After refmac, R = 0.1814 (Rfree = 0.000) for 16992 atoms. Found 81 (81 requested) and removed 68 (40 requested) atoms. Cycle 43: After refmac, R = 0.1733 (Rfree = 0.000) for 16951 atoms. Found 79 (80 requested) and removed 71 (40 requested) atoms. Cycle 44: After refmac, R = 0.1269 (Rfree = 0.000) for 16915 atoms. Found 21 (80 requested) and removed 49 (40 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1173 (Rfree = 0.000) for 16848 atoms. Found 20 (80 requested) and removed 50 (40 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.92 3.67 Search for helices and strands: 0 residues in 0 chains, 17222 seeds are put forward NCS extension: 10 residues added (2 deleted due to clashes), 17232 seeds are put forward Round 1: 635 peptides, 138 chains. Longest chain 11 peptides. Score 0.230 Round 2: 712 peptides, 129 chains. Longest chain 13 peptides. Score 0.310 Round 3: 720 peptides, 130 chains. Longest chain 13 peptides. Score 0.313 Round 4: 732 peptides, 125 chains. Longest chain 16 peptides. Score 0.335 Round 5: 715 peptides, 125 chains. Longest chain 18 peptides. Score 0.324 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 125, Residues 607, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2prr-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 22829 reflections ( 97.72 % complete ) and 40598 restraints for refining 16948 atoms. 38295 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1700 (Rfree = 0.000) for 16948 atoms. Found 0 (80 requested) and removed 40 (40 requested) atoms. Cycle 47: After refmac, R = 0.1825 (Rfree = 0.000) for 16852 atoms. Found 0 (80 requested) and removed 40 (40 requested) atoms. Cycle 48: After refmac, R = 0.1720 (Rfree = 0.000) for 16774 atoms. Found 0 (79 requested) and removed 39 (39 requested) atoms. Cycle 49: After refmac, R = 0.1252 (Rfree = 0.000) for 16695 atoms. TimeTaking 153.05