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-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pim-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pim-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-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/2pim-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-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 19:28:07 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-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pim-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 110 and 0 Target number of residues in the AU: 110 Target solvent content: 0.6443 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-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: 177 Cell parameters: 111.771 111.771 46.411 90.000 90.000 120.000 Input sequence file: 2pim-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 1128 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: 96.797 3.801 Wilson plot Bfac: 72.74 1883 reflections ( 99.11 % complete ) and 0 restraints for refining 1256 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3354 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3243 (Rfree = 0.000) for 1256 atoms. Found 6 (6 requested) and removed 21 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 1270 seeds are put forward Round 1: 73 peptides, 12 chains. Longest chain 19 peptides. Score 0.430 Round 2: 84 peptides, 12 chains. Longest chain 14 peptides. Score 0.526 Round 3: 101 peptides, 9 chains. Longest chain 32 peptides. Score 0.729 Round 4: 102 peptides, 8 chains. Longest chain 24 peptides. Score 0.758 Round 5: 102 peptides, 10 chains. Longest chain 34 peptides. Score 0.709 Taking the results from Round 4 Chains 8, Residues 94, Estimated correctness of the model 59.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1883 reflections ( 99.11 % complete ) and 2164 restraints for refining 1020 atoms. 1796 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2450 (Rfree = 0.000) for 1020 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. Cycle 2: After refmac, R = 0.2240 (Rfree = 0.000) for 998 atoms. Found 4 (5 requested) and removed 4 (2 requested) atoms. Cycle 3: After refmac, R = 0.2354 (Rfree = 0.000) for 992 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 4: After refmac, R = 0.2209 (Rfree = 0.000) for 988 atoms. Found 3 (5 requested) and removed 14 (2 requested) atoms. Cycle 5: After refmac, R = 0.2191 (Rfree = 0.000) for 975 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.54 3.36 Search for helices and strands: 0 residues in 0 chains, 1024 seeds are put forward Round 1: 94 peptides, 10 chains. Longest chain 23 peptides. Score 0.662 Round 2: 99 peptides, 9 chains. Longest chain 24 peptides. Score 0.718 Round 3: 93 peptides, 9 chains. Longest chain 51 peptides. Score 0.684 Round 4: 89 peptides, 10 chains. Longest chain 19 peptides. Score 0.630 Round 5: 83 peptides, 8 chains. Longest chain 42 peptides. Score 0.652 Taking the results from Round 2 Chains 10, Residues 90, Estimated correctness of the model 46.6 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 1883 reflections ( 99.11 % complete ) and 2018 restraints for refining 1003 atoms. 1632 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2592 (Rfree = 0.000) for 1003 atoms. Found 4 (4 requested) and removed 35 (2 requested) atoms. Cycle 7: After refmac, R = 0.2527 (Rfree = 0.000) for 964 atoms. Found 3 (4 requested) and removed 8 (2 requested) atoms. Failed to save intermediate PDB Cycle 8: After refmac, R = 0.2399 (Rfree = 0.000) for 950 atoms. Found 4 (4 requested) and removed 3 (2 requested) atoms. Cycle 9: After refmac, R = 0.2261 (Rfree = 0.000) for 941 atoms. Found 3 (4 requested) and removed 3 (2 requested) atoms. Cycle 10: After refmac, R = 0.2193 (Rfree = 0.000) for 937 atoms. Found 1 (4 requested) and removed 10 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.50 3.32 Search for helices and strands: 0 residues in 0 chains, 955 seeds are put forward Round 1: 77 peptides, 11 chains. Longest chain 16 peptides. Score 0.504 Round 2: 84 peptides, 8 chains. Longest chain 23 peptides. Score 0.658 Round 3: 93 peptides, 10 chains. Longest chain 24 peptides. Score 0.656 Round 4: 92 peptides, 9 chains. Longest chain 27 peptides. Score 0.678 Round 5: 99 peptides, 9 chains. Longest chain 47 peptides. Score 0.718 Taking the results from Round 5 Chains 9, Residues 90, Estimated correctness of the model 46.6 % 2 chains (54 residues) have been docked in sequence Building loops using Loopy2018 9 chains (90 residues) following loop building 2 chains (54 residues) in sequence following loop building ------------------------------------------------------ Failed to save intermediate PDB 1883 reflections ( 99.11 % complete ) and 1639 restraints for refining 1020 atoms. 1116 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2861 (Rfree = 0.000) for 1020 atoms. Found 4 (4 requested) and removed 23 (2 requested) atoms. Cycle 12: After refmac, R = 0.2656 (Rfree = 0.000) for 976 atoms. Found 4 (4 requested) and removed 14 (2 requested) atoms. Cycle 13: After refmac, R = 0.2512 (Rfree = 0.000) for 955 atoms. Found 3 (4 requested) and removed 5 (2 requested) atoms. Failed to save intermediate PDB Cycle 14: After refmac, R = 0.2351 (Rfree = 0.000) for 949 atoms. Found 0 (4 requested) and removed 2 (2 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2356 (Rfree = 0.000) for 945 atoms. Found 2 (4 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.39 3.21 Search for helices and strands: 0 residues in 0 chains, 966 seeds are put forward Round 1: 87 peptides, 10 chains. Longest chain 19 peptides. Score 0.616 Round 2: 94 peptides, 9 chains. Longest chain 36 peptides. Score 0.690 Round 3: 86 peptides, 8 chains. Longest chain 20 peptides. Score 0.671 Round 4: 82 peptides, 6 chains. Longest chain 49 peptides. Score 0.705 Round 5: 78 peptides, 9 chains. Longest chain 26 peptides. Score 0.584 Taking the results from Round 4 Chains 8, Residues 76, Estimated correctness of the model 42.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 1883 reflections ( 99.11 % complete ) and 2114 restraints for refining 1003 atoms. 1790 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2464 (Rfree = 0.000) for 1003 atoms. Found 3 (3 requested) and removed 8 (2 requested) atoms. Cycle 17: After refmac, R = 0.2290 (Rfree = 0.000) for 992 atoms. Found 0 (3 requested) and removed 9 (2 requested) atoms. Failed to save intermediate PDB Cycle 18: After refmac, R = 0.2155 (Rfree = 0.000) for 979 atoms. Found 3 (3 requested) and removed 5 (2 requested) atoms. Failed to save intermediate PDB Cycle 19: After refmac, R = 0.1702 (Rfree = 0.000) for 975 atoms. Found 1 (3 requested) and removed 5 (2 requested) atoms. Failed to save intermediate PDB Cycle 20: After refmac, R = 0.1701 (Rfree = 0.000) for 970 atoms. Found 1 (3 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 3.29 Search for helices and strands: 0 residues in 0 chains, 996 seeds are put forward Round 1: 67 peptides, 12 chains. Longest chain 14 peptides. Score 0.373 Round 2: 76 peptides, 10 chains. Longest chain 21 peptides. Score 0.533 Round 3: 72 peptides, 9 chains. Longest chain 16 peptides. Score 0.538 Round 4: 77 peptides, 9 chains. Longest chain 22 peptides. Score 0.577 Round 5: 77 peptides, 8 chains. Longest chain 16 peptides. Score 0.611 Taking the results from Round 5 Chains 8, Residues 69, Estimated correctness of the model 3.8 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 1883 reflections ( 99.11 % complete ) and 2136 restraints for refining 1018 atoms. 1810 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2605 (Rfree = 0.000) for 1018 atoms. Found 3 (3 requested) and removed 13 (2 requested) atoms. Cycle 22: After refmac, R = 0.2075 (Rfree = 0.000) for 998 atoms. Found 3 (3 requested) and removed 4 (2 requested) atoms. Cycle 23: After refmac, R = 0.1944 (Rfree = 0.000) for 992 atoms. Found 2 (3 requested) and removed 3 (2 requested) atoms. Cycle 24: After refmac, R = 0.1772 (Rfree = 0.000) for 989 atoms. Found 3 (3 requested) and removed 6 (2 requested) atoms. Failed to save intermediate PDB Cycle 25: After refmac, R = 0.1754 (Rfree = 0.000) for 985 atoms. Found 3 (3 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 3.25 Search for helices and strands: 0 residues in 0 chains, 1007 seeds are put forward Round 1: 70 peptides, 13 chains. Longest chain 8 peptides. Score 0.361 Round 2: 77 peptides, 11 chains. Longest chain 19 peptides. Score 0.504 Round 3: 80 peptides, 10 chains. Longest chain 16 peptides. Score 0.565 Round 4: 75 peptides, 8 chains. Longest chain 19 peptides. Score 0.597 Round 5: 86 peptides, 10 chains. Longest chain 21 peptides. Score 0.609 Taking the results from Round 5 Chains 12, Residues 76, Estimated correctness of the model 2.9 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 1883 reflections ( 99.11 % complete ) and 2047 restraints for refining 1020 atoms. 1702 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2722 (Rfree = 0.000) for 1020 atoms. Found 3 (3 requested) and removed 13 (2 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2172 (Rfree = 0.000) for 1003 atoms. Found 3 (3 requested) and removed 4 (2 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2412 (Rfree = 0.000) for 1000 atoms. Found 3 (3 requested) and removed 5 (2 requested) atoms. Failed to save intermediate PDB Cycle 29: After refmac, R = 0.2232 (Rfree = 0.000) for 992 atoms. Found 2 (3 requested) and removed 6 (2 requested) atoms. Cycle 30: After refmac, R = 0.2097 (Rfree = 0.000) for 982 atoms. Found 1 (3 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.23 Search for helices and strands: 0 residues in 0 chains, 1025 seeds are put forward Round 1: 79 peptides, 14 chains. Longest chain 12 peptides. Score 0.406 Round 2: 88 peptides, 11 chains. Longest chain 26 peptides. Score 0.591 Round 3: 84 peptides, 10 chains. Longest chain 27 peptides. Score 0.595 Round 4: 86 peptides, 14 chains. Longest chain 14 peptides. Score 0.469 Round 5: 91 peptides, 12 chains. Longest chain 27 peptides. Score 0.580 Taking the results from Round 3 Chains 12, Residues 74, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 1883 reflections ( 99.11 % complete ) and 2064 restraints for refining 1020 atoms. 1739 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3171 (Rfree = 0.000) for 1020 atoms. Found 3 (3 requested) and removed 35 (2 requested) atoms. Cycle 32: After refmac, R = 0.2792 (Rfree = 0.000) for 973 atoms. Found 3 (3 requested) and removed 22 (2 requested) atoms. Cycle 33: After refmac, R = 0.3186 (Rfree = 0.000) for 946 atoms. Found 3 (3 requested) and removed 22 (2 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.2573 (Rfree = 0.000) for 921 atoms. Found 3 (3 requested) and removed 5 (2 requested) atoms. Cycle 35: After refmac, R = 0.2818 (Rfree = 0.000) for 916 atoms. Found 3 (3 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 979 seeds are put forward Round 1: 57 peptides, 10 chains. Longest chain 11 peptides. Score 0.359 Round 2: 63 peptides, 10 chains. Longest chain 13 peptides. Score 0.419 Round 3: 64 peptides, 10 chains. Longest chain 14 peptides. Score 0.428 Round 4: 63 peptides, 9 chains. Longest chain 12 peptides. Score 0.460 Round 5: 65 peptides, 8 chains. Longest chain 12 peptides. Score 0.518 Taking the results from Round 5 Chains 9, Residues 57, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 1883 reflections ( 99.11 % complete ) and 2165 restraints for refining 997 atoms. 1927 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3612 (Rfree = 0.000) for 997 atoms. Found 3 (3 requested) and removed 41 (2 requested) atoms. Failed to save intermediate PDB Cycle 37: After refmac, R = 0.3235 (Rfree = 0.000) for 945 atoms. Found 3 (3 requested) and removed 20 (2 requested) atoms. Failed to save intermediate PDB Cycle 38: After refmac, R = 0.4017 (Rfree = 0.000) for 915 atoms. Found 3 (3 requested) and removed 35 (2 requested) atoms. Cycle 39: After refmac, R = 0.3557 (Rfree = 0.000) for 874 atoms. Found 2 (2 requested) and removed 14 (2 requested) atoms. Cycle 40: After refmac, R = 0.3593 (Rfree = 0.000) for 860 atoms. Found 2 (2 requested) and removed 16 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.57 3.38 Search for helices and strands: 0 residues in 0 chains, 908 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 6 peptides. Score 0.240 Round 2: 51 peptides, 8 chains. Longest chain 11 peptides. Score 0.388 Round 3: 51 peptides, 9 chains. Longest chain 10 peptides. Score 0.342 Round 4: 59 peptides, 10 chains. Longest chain 11 peptides. Score 0.380 Round 5: 59 peptides, 8 chains. Longest chain 19 peptides. Score 0.465 Taking the results from Round 5 Chains 9, Residues 51, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 1883 reflections ( 99.11 % complete ) and 1895 restraints for refining 949 atoms. 1663 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3666 (Rfree = 0.000) for 949 atoms. Found 3 (3 requested) and removed 34 (2 requested) atoms. Cycle 42: After refmac, R = 0.3794 (Rfree = 0.000) for 911 atoms. Found 3 (3 requested) and removed 34 (2 requested) atoms. Cycle 43: After refmac, R = 0.3804 (Rfree = 0.000) for 874 atoms. Found 2 (2 requested) and removed 20 (2 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.3503 (Rfree = 0.000) for 851 atoms. Found 2 (2 requested) and removed 7 (2 requested) atoms. Cycle 45: After refmac, R = 0.3656 (Rfree = 0.000) for 843 atoms. Found 2 (2 requested) and removed 41 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.80 3.60 Search for helices and strands: 0 residues in 0 chains, 851 seeds are put forward Round 1: 44 peptides, 11 chains. Longest chain 4 peptides. Score 0.167 Round 2: 59 peptides, 13 chains. Longest chain 7 peptides. Score 0.246 Round 3: 55 peptides, 12 chains. Longest chain 8 peptides. Score 0.248 Round 4: 59 peptides, 10 chains. Longest chain 10 peptides. Score 0.380 Round 5: 58 peptides, 8 chains. Longest chain 21 peptides. Score 0.456 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 50, 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 2pim-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1883 reflections ( 99.11 % complete ) and 1914 restraints for refining 883 atoms. 1722 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3772 (Rfree = 0.000) for 883 atoms. Found 0 (2 requested) and removed 2 (2 requested) atoms. Cycle 47: After refmac, R = 0.3691 (Rfree = 0.000) for 878 atoms. Found 0 (2 requested) and removed 2 (2 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2980 (Rfree = 0.000) for 870 atoms. Found 0 (2 requested) and removed 2 (2 requested) atoms. Cycle 49: After refmac, R = 0.2753 (Rfree = 0.000) for 866 atoms. Found 0 (2 requested) and removed 2 (2 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:05:53 GMT 2018 Job finished. TimeTaking 37.93