Tue 25 Dec 19:27:57 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 2pim-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pim-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pim-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-4.0-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/2pim-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-4.0-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 19:28:07 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/2pim-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-4.0-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 108 and 0 Target number of residues in the AU: 108 Target solvent content: 0.6508 Checking the provided sequence file Detected sequence length: 141 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 141 Adjusted target solvent content: 0.54 Input MTZ file: 2pim-4.0-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: 177 Cell parameters: 111.771 111.771 46.411 90.000 90.000 120.000 Input sequence file: 2pim-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1128 target number of atoms Had to go as low as 0.70 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: 96.797 4.001 Wilson plot Bfac: 77.10 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1627 reflections ( 98.97 % complete ) and 0 restraints for refining 1243 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3564 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3242 (Rfree = 0.000) for 1243 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 1268 seeds are put forward Round 1: 63 peptides, 12 chains. Longest chain 10 peptides. Score 0.333 Round 2: 77 peptides, 13 chains. Longest chain 10 peptides. Score 0.427 Round 3: 82 peptides, 12 chains. Longest chain 12 peptides. Score 0.509 Round 4: 88 peptides, 12 chains. Longest chain 10 peptides. Score 0.557 Round 5: 82 peptides, 9 chains. Longest chain 15 peptides. Score 0.613 Taking the results from Round 5 Chains 11, Residues 73, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 1627 reflections ( 98.97 % complete ) and 2204 restraints for refining 1017 atoms. 1866 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2835 (Rfree = 0.000) for 1017 atoms. Found 4 (4 requested) and removed 16 (2 requested) atoms. Cycle 2: After refmac, R = 0.2473 (Rfree = 0.000) for 970 atoms. Found 2 (4 requested) and removed 11 (2 requested) atoms. Cycle 3: After refmac, R = 0.2426 (Rfree = 0.000) for 945 atoms. Found 4 (4 requested) and removed 6 (2 requested) atoms. Cycle 4: After refmac, R = 0.2388 (Rfree = 0.000) for 940 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 5: After refmac, R = 0.2225 (Rfree = 0.000) for 938 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.68 3.49 Search for helices and strands: 0 residues in 0 chains, 963 seeds are put forward Round 1: 70 peptides, 12 chains. Longest chain 13 peptides. Score 0.402 Round 2: 90 peptides, 12 chains. Longest chain 16 peptides. Score 0.572 Round 3: 88 peptides, 12 chains. Longest chain 18 peptides. Score 0.557 Round 4: 89 peptides, 10 chains. Longest chain 21 peptides. Score 0.630 Round 5: 97 peptides, 12 chains. Longest chain 19 peptides. Score 0.622 Taking the results from Round 4 Chains 11, Residues 79, Estimated correctness of the model 0.0 % 2 chains (16 residues) have been docked in sequence ------------------------------------------------------ 1627 reflections ( 98.97 % complete ) and 2101 restraints for refining 1018 atoms. 1750 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2615 (Rfree = 0.000) for 1018 atoms. Found 3 (4 requested) and removed 10 (2 requested) atoms. Cycle 7: After refmac, R = 0.2210 (Rfree = 0.000) for 999 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2051 (Rfree = 0.000) for 991 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 9: After refmac, R = 0.1991 (Rfree = 0.000) for 985 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Failed to save intermediate PDB Cycle 10: After refmac, R = 0.1978 (Rfree = 0.000) for 981 atoms. Found 1 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.60 3.41 Search for helices and strands: 0 residues in 0 chains, 1025 seeds are put forward Round 1: 67 peptides, 11 chains. Longest chain 12 peptides. Score 0.415 Round 2: 81 peptides, 10 chains. Longest chain 18 peptides. Score 0.572 Round 3: 81 peptides, 11 chains. Longest chain 12 peptides. Score 0.537 Round 4: 85 peptides, 10 chains. Longest chain 16 peptides. Score 0.602 Round 5: 84 peptides, 10 chains. Longest chain 20 peptides. Score 0.595 Taking the results from Round 4 Chains 11, Residues 75, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 1627 reflections ( 98.97 % complete ) and 2298 restraints for refining 1018 atoms. 1987 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2817 (Rfree = 0.000) for 1018 atoms. Found 1 (4 requested) and removed 8 (2 requested) atoms. Cycle 12: After refmac, R = 0.2201 (Rfree = 0.000) for 1004 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. Failed to save intermediate PDB Cycle 13: After refmac, R = 0.2189 (Rfree = 0.000) for 998 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Cycle 14: After refmac, R = 0.2067 (Rfree = 0.000) for 996 atoms. Found 1 (4 requested) and removed 5 (2 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.1945 (Rfree = 0.000) for 991 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.60 3.41 Search for helices and strands: 0 residues in 0 chains, 1041 seeds are put forward Round 1: 51 peptides, 9 chains. Longest chain 12 peptides. Score 0.342 Round 2: 75 peptides, 12 chains. Longest chain 13 peptides. Score 0.449 Round 3: 68 peptides, 11 chains. Longest chain 14 peptides. Score 0.424 Round 4: 69 peptides, 9 chains. Longest chain 14 peptides. Score 0.513 Round 5: 75 peptides, 10 chains. Longest chain 15 peptides. Score 0.525 Taking the results from Round 5 Chains 10, Residues 65, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1627 reflections ( 98.97 % complete ) and 2377 restraints for refining 1018 atoms. 2127 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2426 (Rfree = 0.000) for 1018 atoms. Found 2 (4 requested) and removed 7 (2 requested) atoms. Cycle 17: After refmac, R = 0.1979 (Rfree = 0.000) for 1012 atoms. Found 4 (4 requested) and removed 12 (2 requested) atoms. Cycle 18: After refmac, R = 0.1895 (Rfree = 0.000) for 998 atoms. Found 1 (4 requested) and removed 2 (2 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1798 (Rfree = 0.000) for 995 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1698 (Rfree = 0.000) for 992 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.48 Search for helices and strands: 0 residues in 0 chains, 1024 seeds are put forward Round 1: 70 peptides, 14 chains. Longest chain 8 peptides. Score 0.318 Round 2: 71 peptides, 12 chains. Longest chain 13 peptides. Score 0.412 Round 3: 73 peptides, 12 chains. Longest chain 12 peptides. Score 0.430 Round 4: 74 peptides, 8 chains. Longest chain 23 peptides. Score 0.589 Round 5: 69 peptides, 10 chains. Longest chain 13 peptides. Score 0.474 Taking the results from Round 4 Chains 8, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 1627 reflections ( 98.97 % complete ) and 2349 restraints for refining 1016 atoms. 2093 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3293 (Rfree = 0.000) for 1016 atoms. Found 4 (4 requested) and removed 29 (2 requested) atoms. Cycle 22: After refmac, R = 0.2452 (Rfree = 0.000) for 976 atoms. Found 3 (4 requested) and removed 2 (2 requested) atoms. Cycle 23: After refmac, R = 0.2283 (Rfree = 0.000) for 969 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 24: After refmac, R = 0.2210 (Rfree = 0.000) for 959 atoms. Found 1 (4 requested) and removed 6 (2 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.2325 (Rfree = 0.000) for 952 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 993 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 7 peptides. Score 0.280 Round 2: 68 peptides, 10 chains. Longest chain 14 peptides. Score 0.465 Round 3: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.366 Round 4: 66 peptides, 11 chains. Longest chain 8 peptides. Score 0.405 Round 5: 73 peptides, 11 chains. Longest chain 19 peptides. Score 0.470 Taking the results from Round 5 Chains 11, Residues 62, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1627 reflections ( 98.97 % complete ) and 2283 restraints for refining 981 atoms. 2046 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2612 (Rfree = 0.000) for 981 atoms. Found 2 (4 requested) and removed 10 (2 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2149 (Rfree = 0.000) for 966 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 28: After refmac, R = 0.2020 (Rfree = 0.000) for 960 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. Cycle 29: After refmac, R = 0.2015 (Rfree = 0.000) for 959 atoms. Found 2 (4 requested) and removed 11 (2 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2028 (Rfree = 0.000) for 948 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.56 3.37 Search for helices and strands: 0 residues in 0 chains, 989 seeds are put forward Round 1: 52 peptides, 9 chains. Longest chain 9 peptides. Score 0.353 Round 2: 65 peptides, 11 chains. Longest chain 9 peptides. Score 0.396 Round 3: 74 peptides, 13 chains. Longest chain 11 peptides. Score 0.399 Round 4: 69 peptides, 11 chains. Longest chain 11 peptides. Score 0.434 Round 5: 63 peptides, 10 chains. Longest chain 10 peptides. Score 0.419 Taking the results from Round 4 Chains 11, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1627 reflections ( 98.97 % complete ) and 2198 restraints for refining 961 atoms. 1977 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2193 (Rfree = 0.000) for 961 atoms. Found 4 (4 requested) and removed 27 (2 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2410 (Rfree = 0.000) for 929 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Failed to save intermediate PDB Cycle 33: After refmac, R = 0.2245 (Rfree = 0.000) for 923 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 34: After refmac, R = 0.2056 (Rfree = 0.000) for 920 atoms. Found 0 (4 requested) and removed 7 (2 requested) atoms. Failed to save intermediate PDB Cycle 35: After refmac, R = 0.2059 (Rfree = 0.000) for 911 atoms. Found 4 (4 requested) and removed 10 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.66 3.47 Search for helices and strands: 0 residues in 0 chains, 950 seeds are put forward Round 1: 52 peptides, 12 chains. Longest chain 5 peptides. Score 0.214 Round 2: 62 peptides, 12 chains. Longest chain 9 peptides. Score 0.323 Round 3: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.399 Round 4: 77 peptides, 12 chains. Longest chain 11 peptides. Score 0.467 Round 5: 67 peptides, 10 chains. Longest chain 9 peptides. Score 0.456 Taking the results from Round 4 Chains 12, Residues 65, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 1627 reflections ( 98.97 % complete ) and 2169 restraints for refining 969 atoms. 1909 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2155 (Rfree = 0.000) for 969 atoms. Found 4 (4 requested) and removed 9 (2 requested) atoms. Cycle 37: After refmac, R = 0.1897 (Rfree = 0.000) for 962 atoms. Found 1 (4 requested) and removed 3 (2 requested) atoms. Cycle 38: After refmac, R = 0.1902 (Rfree = 0.000) for 955 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2213 (Rfree = 0.000) for 943 atoms. Found 2 (4 requested) and removed 4 (2 requested) atoms. Cycle 40: After refmac, R = 0.2232 (Rfree = 0.000) for 937 atoms. Found 2 (4 requested) and removed 9 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.35 Search for helices and strands: 0 residues in 0 chains, 981 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.283 Round 2: 61 peptides, 11 chains. Longest chain 9 peptides. Score 0.356 Round 3: 63 peptides, 11 chains. Longest chain 9 peptides. Score 0.376 Round 4: 57 peptides, 10 chains. Longest chain 10 peptides. Score 0.359 Round 5: 60 peptides, 10 chains. Longest chain 10 peptides. Score 0.389 Taking the results from Round 5 Chains 10, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1627 reflections ( 98.97 % complete ) and 2317 restraints for refining 975 atoms. 2127 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2511 (Rfree = 0.000) for 975 atoms. Found 4 (4 requested) and removed 42 (2 requested) atoms. Cycle 42: After refmac, R = 0.3002 (Rfree = 0.000) for 923 atoms. Found 4 (4 requested) and removed 18 (2 requested) atoms. Cycle 43: After refmac, R = 0.2472 (Rfree = 0.000) for 898 atoms. Found 4 (4 requested) and removed 4 (2 requested) atoms. Cycle 44: After refmac, R = 0.2576 (Rfree = 0.000) for 893 atoms. Found 4 (4 requested) and removed 7 (2 requested) atoms. Cycle 45: After refmac, R = 0.2526 (Rfree = 0.000) for 889 atoms. Found 4 (4 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.72 3.53 Search for helices and strands: 0 residues in 0 chains, 943 seeds are put forward Round 1: 39 peptides, 9 chains. Longest chain 5 peptides. Score 0.205 Round 2: 55 peptides, 10 chains. Longest chain 9 peptides. Score 0.339 Round 3: 55 peptides, 11 chains. Longest chain 7 peptides. Score 0.293 Round 4: 66 peptides, 11 chains. Longest chain 10 peptides. Score 0.405 Round 5: 60 peptides, 11 chains. Longest chain 8 peptides. Score 0.346 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 11, Residues 55, Estimated correctness of the model 0.0 % 2 chains (13 residues) have been docked in sequence Sequence coverage is 23 % Consider running further cycles of model building using 2pim-4_warpNtrace.pdb as input Building loops using Loopy2018 11 chains (55 residues) following loop building 2 chains (13 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1627 reflections ( 98.97 % complete ) and 1913 restraints for refining 935 atoms. 1663 conditional restraints added. Observations/parameters ratio is 0.44 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2787 (Rfree = 0.000) for 935 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.2941 (Rfree = 0.000) for 912 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Cycle 48: After refmac, R = 0.2863 (Rfree = 0.000) for 900 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.2802 (Rfree = 0.000) for 893 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:04:35 GMT 2018 Job finished. TimeTaking 36.63