Tue 25 Dec 19:27:58 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ilb-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ilb-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ilb-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-3.8-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-3.8-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:06 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/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ilb-3.8-parrot-hancs/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 67 and 0 Target number of residues in the AU: 67 Target solvent content: 0.6636 Checking the provided sequence file Detected sequence length: 114 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 114 Adjusted target solvent content: 0.43 Input MTZ file: 2ilb-3.8-parrot-hancs.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: 5 Cell parameters: 48.900 72.000 32.740 90.000 110.754 90.000 Input sequence file: 2ilb-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 912 target number of atoms Had to go as low as 0.75 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 Loops will be built when appropriate and at the last cycle Resolution range: 38.600 3.802 Wilson plot Bfac: 85.75 Failed to save intermediate PDB 1069 reflections ( 99.53 % complete ) and 0 restraints for refining 1004 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3434 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2642 (Rfree = 0.000) for 1004 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.58 3.93 Search for helices and strands: 0 residues in 0 chains, 1013 seeds are put forward Round 1: 33 peptides, 7 chains. Longest chain 8 peptides. Score 0.258 Round 2: 39 peptides, 6 chains. Longest chain 14 peptides. Score 0.425 Round 3: 36 peptides, 5 chains. Longest chain 15 peptides. Score 0.447 Round 4: 35 peptides, 5 chains. Longest chain 12 peptides. Score 0.432 Round 5: 33 peptides, 5 chains. Longest chain 10 peptides. Score 0.402 Taking the results from Round 3 Chains 5, Residues 31, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1069 reflections ( 99.53 % complete ) and 2033 restraints for refining 825 atoms. 1914 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2505 (Rfree = 0.000) for 825 atoms. Found 4 (4 requested) and removed 14 (2 requested) atoms. Cycle 2: After refmac, R = 0.2668 (Rfree = 0.000) for 809 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 3: After refmac, R = 0.2286 (Rfree = 0.000) for 804 atoms. Found 4 (4 requested) and removed 12 (2 requested) atoms. Cycle 4: After refmac, R = 0.2177 (Rfree = 0.000) for 796 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 5: After refmac, R = 0.2349 (Rfree = 0.000) for 792 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.71 4.08 Search for helices and strands: 0 residues in 0 chains, 809 seeds are put forward Round 1: 43 peptides, 8 chains. Longest chain 8 peptides. Score 0.354 Round 2: 46 peptides, 8 chains. Longest chain 8 peptides. Score 0.399 Round 3: 53 peptides, 7 chains. Longest chain 16 peptides. Score 0.553 Round 4: 52 peptides, 8 chains. Longest chain 11 peptides. Score 0.484 Round 5: 48 peptides, 7 chains. Longest chain 12 peptides. Score 0.489 Taking the results from Round 3 Chains 7, Residues 46, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1069 reflections ( 99.53 % complete ) and 1907 restraints for refining 804 atoms. 1730 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2398 (Rfree = 0.000) for 804 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 7: After refmac, R = 0.2231 (Rfree = 0.000) for 803 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 8: After refmac, R = 0.2707 (Rfree = 0.000) for 801 atoms. Found 2 (4 requested) and removed 6 (2 requested) atoms. Cycle 9: After refmac, R = 0.2482 (Rfree = 0.000) for 796 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 10: After refmac, R = 0.2417 (Rfree = 0.000) for 792 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.61 3.97 Search for helices and strands: 0 residues in 0 chains, 804 seeds are put forward Round 1: 32 peptides, 7 chains. Longest chain 7 peptides. Score 0.241 Round 2: 40 peptides, 7 chains. Longest chain 8 peptides. Score 0.374 Round 3: 39 peptides, 5 chains. Longest chain 15 peptides. Score 0.490 Round 4: 45 peptides, 6 chains. Longest chain 16 peptides. Score 0.509 Round 5: 47 peptides, 6 chains. Longest chain 17 peptides. Score 0.535 Taking the results from Round 5 Chains 6, Residues 41, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 1069 reflections ( 99.53 % complete ) and 1894 restraints for refining 820 atoms. 1718 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2410 (Rfree = 0.000) for 820 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 12: After refmac, R = 0.2167 (Rfree = 0.000) for 817 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 13: After refmac, R = 0.2114 (Rfree = 0.000) for 811 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 14: After refmac, R = 0.2177 (Rfree = 0.000) for 809 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 15: After refmac, R = 0.1988 (Rfree = 0.000) for 806 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.71 4.08 Search for helices and strands: 0 residues in 0 chains, 835 seeds are put forward Round 1: 33 peptides, 7 chains. Longest chain 7 peptides. Score 0.258 Round 2: 42 peptides, 8 chains. Longest chain 8 peptides. Score 0.338 Round 3: 42 peptides, 7 chains. Longest chain 12 peptides. Score 0.404 Round 4: 38 peptides, 7 chains. Longest chain 9 peptides. Score 0.342 Round 5: 38 peptides, 7 chains. Longest chain 12 peptides. Score 0.342 Taking the results from Round 3 Chains 7, Residues 35, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1069 reflections ( 99.53 % complete ) and 2031 restraints for refining 825 atoms. 1898 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2029 (Rfree = 0.000) for 825 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 17: After refmac, R = 0.1936 (Rfree = 0.000) for 819 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 18: After refmac, R = 0.2506 (Rfree = 0.000) for 815 atoms. Found 3 (4 requested) and removed 7 (2 requested) atoms. Cycle 19: After refmac, R = 0.2366 (Rfree = 0.000) for 809 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 20: After refmac, R = 0.2250 (Rfree = 0.000) for 807 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.57 3.92 Search for helices and strands: 0 residues in 0 chains, 825 seeds are put forward Round 1: 35 peptides, 7 chains. Longest chain 7 peptides. Score 0.293 Round 2: 48 peptides, 7 chains. Longest chain 13 peptides. Score 0.489 Round 3: 48 peptides, 7 chains. Longest chain 13 peptides. Score 0.489 Round 4: 52 peptides, 7 chains. Longest chain 15 peptides. Score 0.541 Round 5: 50 peptides, 7 chains. Longest chain 15 peptides. Score 0.516 Taking the results from Round 4 Chains 7, Residues 45, Estimated correctness of the model 0.0 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 1069 reflections ( 99.53 % complete ) and 1781 restraints for refining 825 atoms. 1543 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2711 (Rfree = 0.000) for 825 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 22: After refmac, R = 0.2571 (Rfree = 0.000) for 819 atoms. Found 2 (4 requested) and removed 5 (2 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2550 (Rfree = 0.000) for 815 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 24: After refmac, R = 0.2508 (Rfree = 0.000) for 813 atoms. Found 2 (4 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.2306 (Rfree = 0.000) for 811 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 5.11 5.61 Search for helices and strands: 0 residues in 0 chains, 824 seeds are put forward Round 1: 33 peptides, 8 chains. Longest chain 5 peptides. Score 0.185 Round 2: 45 peptides, 8 chains. Longest chain 8 peptides. Score 0.384 Round 3: 46 peptides, 9 chains. Longest chain 7 peptides. Score 0.335 Round 4: 51 peptides, 9 chains. Longest chain 9 peptides. Score 0.410 Round 5: 51 peptides, 8 chains. Longest chain 9 peptides. Score 0.471 Taking the results from Round 5 Chains 8, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1069 reflections ( 99.53 % complete ) and 1917 restraints for refining 815 atoms. 1753 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2380 (Rfree = 0.000) for 815 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 27: After refmac, R = 0.2216 (Rfree = 0.000) for 814 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 28: After refmac, R = 0.2076 (Rfree = 0.000) for 811 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 29: After refmac, R = 0.2028 (Rfree = 0.000) for 807 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 30: After refmac, R = 0.1943 (Rfree = 0.000) for 806 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.58 3.93 Search for helices and strands: 0 residues in 0 chains, 824 seeds are put forward Round 1: 34 peptides, 8 chains. Longest chain 5 peptides. Score 0.203 Round 2: 37 peptides, 8 chains. Longest chain 6 peptides. Score 0.256 Round 3: 37 peptides, 8 chains. Longest chain 6 peptides. Score 0.256 Round 4: 39 peptides, 7 chains. Longest chain 11 peptides. Score 0.358 Round 5: 37 peptides, 7 chains. Longest chain 8 peptides. Score 0.326 Taking the results from Round 4 Chains 7, Residues 32, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 1069 reflections ( 99.53 % complete ) and 1966 restraints for refining 806 atoms. 1845 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1985 (Rfree = 0.000) for 806 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. Cycle 32: After refmac, R = 0.1807 (Rfree = 0.000) for 807 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 33: After refmac, R = 0.1726 (Rfree = 0.000) for 805 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 34: After refmac, R = 0.1658 (Rfree = 0.000) for 804 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 35: After refmac, R = 0.1615 (Rfree = 0.000) for 803 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.56 3.91 Search for helices and strands: 0 residues in 0 chains, 822 seeds are put forward Round 1: 33 peptides, 7 chains. Longest chain 6 peptides. Score 0.258 Round 2: 37 peptides, 7 chains. Longest chain 7 peptides. Score 0.326 Round 3: 36 peptides, 6 chains. Longest chain 9 peptides. Score 0.379 Round 4: 29 peptides, 5 chains. Longest chain 9 peptides. Score 0.337 Round 5: 33 peptides, 4 chains. Longest chain 18 peptides. Score 0.471 Taking the results from Round 5 Chains 4, Residues 29, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1069 reflections ( 99.53 % complete ) and 1994 restraints for refining 823 atoms. 1882 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1741 (Rfree = 0.000) for 823 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 37: After refmac, R = 0.1661 (Rfree = 0.000) for 821 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 38: After refmac, R = 0.1625 (Rfree = 0.000) for 819 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.1585 (Rfree = 0.000) for 817 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Failed to save intermediate PDB Cycle 40: After refmac, R = 0.1533 (Rfree = 0.000) for 815 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.60 3.95 Search for helices and strands: 0 residues in 0 chains, 826 seeds are put forward Round 1: 29 peptides, 5 chains. Longest chain 9 peptides. Score 0.337 Round 2: 28 peptides, 5 chains. Longest chain 9 peptides. Score 0.320 Round 3: 32 peptides, 6 chains. Longest chain 9 peptides. Score 0.314 Round 4: 30 peptides, 5 chains. Longest chain 9 peptides. Score 0.354 Round 5: 28 peptides, 5 chains. Longest chain 8 peptides. Score 0.320 Taking the results from Round 4 Chains 5, Residues 25, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 1069 reflections ( 99.53 % complete ) and 2009 restraints for refining 820 atoms. 1914 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1681 (Rfree = 0.000) for 820 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 42: After refmac, R = 0.1524 (Rfree = 0.000) for 819 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 43: After refmac, R = 0.1433 (Rfree = 0.000) for 817 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1395 (Rfree = 0.000) for 815 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 45: After refmac, R = 0.1364 (Rfree = 0.000) for 813 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.64 4.00 Search for helices and strands: 0 residues in 0 chains, 825 seeds are put forward Round 1: 23 peptides, 5 chains. Longest chain 7 peptides. Score 0.228 Round 2: 22 peptides, 4 chains. Longest chain 8 peptides. Score 0.292 Round 3: 23 peptides, 4 chains. Longest chain 9 peptides. Score 0.310 Round 4: 24 peptides, 4 chains. Longest chain 9 peptides. Score 0.328 Round 5: 27 peptides, 5 chains. Longest chain 9 peptides. Score 0.303 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 4, Residues 20, 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 2ilb-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1069 reflections ( 99.53 % complete ) and 2038 restraints for refining 810 atoms. 1962 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1487 (Rfree = 0.000) for 810 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.1355 (Rfree = 0.000) for 808 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.1290 (Rfree = 0.000) for 806 atoms. Found 0 (4 requested) and removed 0 (2 requested) atoms. Cycle 49: After refmac, R = 0.1247 (Rfree = 0.000) for 806 atoms. Found 0 (4 requested) and removed 1 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:01:08 GMT 2018 Job finished. TimeTaking 33.17