null Sun 23 Dec 22:23:05 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 2od5-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2od5-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2od5-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-3.4-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/2od5-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-3.4-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 ============================================================ Sun 23 Dec 22:23:15 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/2od5-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-3.4-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: 0.6273 Checking the provided sequence file Detected sequence length: 116 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 116 Adjusted target solvent content: 0.61 Input MTZ file: 2od5-3.4-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: 180 Cell parameters: 64.428 64.428 133.292 90.000 90.000 120.000 Input sequence file: 2od5-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 928 target number of atoms Had to go as low as 0.85 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: 55.796 3.400 Wilson plot Bfac: 65.03 2552 reflections ( 99.69 % complete ) and 0 restraints for refining 1027 atoms. Observations/parameters ratio is 0.62 ------------------------------------------------------ Starting model: R = 0.3743 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3712 (Rfree = 0.000) for 1027 atoms. Found 7 (7 requested) and removed 16 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.26 2.81 Search for helices and strands: 0 residues in 0 chains, 1043 seeds are put forward Round 1: 55 peptides, 10 chains. Longest chain 12 peptides. Score 0.345 Round 2: 66 peptides, 7 chains. Longest chain 19 peptides. Score 0.576 Round 3: 69 peptides, 6 chains. Longest chain 20 peptides. Score 0.635 Round 4: 70 peptides, 6 chains. Longest chain 18 peptides. Score 0.642 Round 5: 69 peptides, 9 chains. Longest chain 16 peptides. Score 0.524 Taking the results from Round 4 Chains 6, Residues 64, Estimated correctness of the model 41.8 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2552 reflections ( 99.69 % complete ) and 1852 restraints for refining 834 atoms. 1602 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3254 (Rfree = 0.000) for 834 atoms. Found 6 (6 requested) and removed 27 (3 requested) atoms. Cycle 2: After refmac, R = 0.2926 (Rfree = 0.000) for 794 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 3: After refmac, R = 0.2879 (Rfree = 0.000) for 785 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 4: After refmac, R = 0.2674 (Rfree = 0.000) for 782 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 5: After refmac, R = 0.2717 (Rfree = 0.000) for 779 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.14 2.71 Search for helices and strands: 0 residues in 0 chains, 828 seeds are put forward Round 1: 63 peptides, 7 chains. Longest chain 20 peptides. Score 0.551 Round 2: 71 peptides, 7 chains. Longest chain 18 peptides. Score 0.615 Round 3: 71 peptides, 7 chains. Longest chain 16 peptides. Score 0.615 Round 4: 72 peptides, 6 chains. Longest chain 17 peptides. Score 0.656 Round 5: 68 peptides, 6 chains. Longest chain 27 peptides. Score 0.628 Taking the results from Round 4 Chains 6, Residues 66, Estimated correctness of the model 45.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2552 reflections ( 99.69 % complete ) and 1673 restraints for refining 793 atoms. 1415 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2951 (Rfree = 0.000) for 793 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 7: After refmac, R = 0.2762 (Rfree = 0.000) for 786 atoms. Found 2 (5 requested) and removed 6 (2 requested) atoms. Cycle 8: After refmac, R = 0.3085 (Rfree = 0.000) for 782 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 9: After refmac, R = 0.2729 (Rfree = 0.000) for 780 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 10: After refmac, R = 0.2564 (Rfree = 0.000) for 775 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.12 2.69 Search for helices and strands: 0 residues in 0 chains, 803 seeds are put forward Round 1: 73 peptides, 8 chains. Longest chain 17 peptides. Score 0.594 Round 2: 74 peptides, 6 chains. Longest chain 20 peptides. Score 0.670 Round 3: 73 peptides, 5 chains. Longest chain 21 peptides. Score 0.695 Round 4: 71 peptides, 4 chains. Longest chain 26 peptides. Score 0.715 Round 5: 64 peptides, 6 chains. Longest chain 21 peptides. Score 0.598 Taking the results from Round 4 Chains 6, Residues 67, Estimated correctness of the model 61.6 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 2552 reflections ( 99.69 % complete ) and 1519 restraints for refining 805 atoms. 1191 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3151 (Rfree = 0.000) for 805 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 12: After refmac, R = 0.3045 (Rfree = 0.000) for 790 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 13: After refmac, R = 0.3534 (Rfree = 0.000) for 786 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 14: After refmac, R = 0.3121 (Rfree = 0.000) for 784 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. Cycle 15: After refmac, R = 0.3404 (Rfree = 0.000) for 785 atoms. Found 5 (5 requested) and removed 6 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.17 2.73 Search for helices and strands: 0 residues in 0 chains, 810 seeds are put forward Round 1: 66 peptides, 7 chains. Longest chain 21 peptides. Score 0.576 Round 2: 71 peptides, 8 chains. Longest chain 16 peptides. Score 0.578 Round 3: 67 peptides, 7 chains. Longest chain 19 peptides. Score 0.584 Round 4: 66 peptides, 6 chains. Longest chain 16 peptides. Score 0.613 Round 5: 71 peptides, 8 chains. Longest chain 15 peptides. Score 0.578 Taking the results from Round 4 Chains 6, Residues 60, Estimated correctness of the model 32.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2552 reflections ( 99.69 % complete ) and 1903 restraints for refining 819 atoms. 1669 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3340 (Rfree = 0.000) for 819 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 17: After refmac, R = 0.3084 (Rfree = 0.000) for 810 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. Cycle 18: After refmac, R = 0.3025 (Rfree = 0.000) for 807 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. Cycle 19: After refmac, R = 0.2884 (Rfree = 0.000) for 807 atoms. Found 1 (6 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.2919 (Rfree = 0.000) for 800 atoms. Found 4 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 830 seeds are put forward Round 1: 58 peptides, 5 chains. Longest chain 16 peptides. Score 0.589 Round 2: 56 peptides, 6 chains. Longest chain 14 peptides. Score 0.532 Round 3: 65 peptides, 7 chains. Longest chain 15 peptides. Score 0.568 Round 4: 62 peptides, 7 chains. Longest chain 17 peptides. Score 0.543 Round 5: 63 peptides, 7 chains. Longest chain 14 peptides. Score 0.551 Taking the results from Round 1 Chains 5, Residues 53, Estimated correctness of the model 25.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2552 reflections ( 99.69 % complete ) and 1773 restraints for refining 791 atoms. 1566 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3015 (Rfree = 0.000) for 791 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 22: After refmac, R = 0.2826 (Rfree = 0.000) for 791 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 23: After refmac, R = 0.2742 (Rfree = 0.000) for 792 atoms. Found 4 (5 requested) and removed 3 (2 requested) atoms. Cycle 24: After refmac, R = 0.2785 (Rfree = 0.000) for 791 atoms. Found 1 (5 requested) and removed 2 (2 requested) atoms. Cycle 25: After refmac, R = 0.2715 (Rfree = 0.000) for 789 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.17 2.73 Search for helices and strands: 0 residues in 0 chains, 811 seeds are put forward Round 1: 60 peptides, 8 chains. Longest chain 11 peptides. Score 0.484 Round 2: 67 peptides, 8 chains. Longest chain 17 peptides. Score 0.546 Round 3: 62 peptides, 7 chains. Longest chain 12 peptides. Score 0.543 Round 4: 65 peptides, 7 chains. Longest chain 13 peptides. Score 0.568 Round 5: 68 peptides, 9 chains. Longest chain 13 peptides. Score 0.515 Taking the results from Round 4 Chains 7, Residues 58, Estimated correctness of the model 17.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2552 reflections ( 99.69 % complete ) and 1778 restraints for refining 790 atoms. 1553 conditional restraints added. Observations/parameters ratio is 0.81 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2957 (Rfree = 0.000) for 790 atoms. Found 5 (5 requested) and removed 3 (2 requested) atoms. Cycle 27: After refmac, R = 0.2805 (Rfree = 0.000) for 790 atoms. Found 2 (5 requested) and removed 3 (2 requested) atoms. Cycle 28: After refmac, R = 0.2781 (Rfree = 0.000) for 785 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 29: After refmac, R = 0.2752 (Rfree = 0.000) for 782 atoms. Found 3 (5 requested) and removed 4 (2 requested) atoms. Cycle 30: After refmac, R = 0.2739 (Rfree = 0.000) for 779 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.17 2.73 Search for helices and strands: 0 residues in 0 chains, 815 seeds are put forward Round 1: 65 peptides, 6 chains. Longest chain 20 peptides. Score 0.606 Round 2: 70 peptides, 5 chains. Longest chain 19 peptides. Score 0.676 Round 3: 70 peptides, 6 chains. Longest chain 20 peptides. Score 0.642 Round 4: 72 peptides, 7 chains. Longest chain 20 peptides. Score 0.622 Round 5: 70 peptides, 5 chains. Longest chain 26 peptides. Score 0.676 Taking the results from Round 5 Chains 6, Residues 65, Estimated correctness of the model 51.5 % 2 chains (34 residues) have been docked in sequence ------------------------------------------------------ 2552 reflections ( 99.69 % complete ) and 1421 restraints for refining 844 atoms. 1020 conditional restraints added. Observations/parameters ratio is 0.76 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3067 (Rfree = 0.000) for 844 atoms. Found 4 (6 requested) and removed 18 (3 requested) atoms. Cycle 32: After refmac, R = 0.2915 (Rfree = 0.000) for 820 atoms. Found 3 (6 requested) and removed 7 (3 requested) atoms. Cycle 33: After refmac, R = 0.2742 (Rfree = 0.000) for 812 atoms. Found 3 (6 requested) and removed 5 (3 requested) atoms. Cycle 34: After refmac, R = 0.2870 (Rfree = 0.000) for 806 atoms. Found 5 (6 requested) and removed 4 (3 requested) atoms. Cycle 35: After refmac, R = 0.2803 (Rfree = 0.000) for 802 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.12 2.69 Search for helices and strands: 0 residues in 0 chains, 829 seeds are put forward Round 1: 57 peptides, 7 chains. Longest chain 18 peptides. Score 0.499 Round 2: 66 peptides, 6 chains. Longest chain 20 peptides. Score 0.613 Round 3: 57 peptides, 5 chains. Longest chain 17 peptides. Score 0.581 Round 4: 72 peptides, 6 chains. Longest chain 27 peptides. Score 0.656 Round 5: 73 peptides, 6 chains. Longest chain 24 peptides. Score 0.663 Taking the results from Round 5 Chains 6, Residues 67, Estimated correctness of the model 47.9 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2552 reflections ( 99.69 % complete ) and 1806 restraints for refining 821 atoms. 1544 conditional restraints added. Observations/parameters ratio is 0.78 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2999 (Rfree = 0.000) for 821 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 37: After refmac, R = 0.2691 (Rfree = 0.000) for 818 atoms. Found 1 (6 requested) and removed 5 (3 requested) atoms. Cycle 38: After refmac, R = 0.2565 (Rfree = 0.000) for 814 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 39: After refmac, R = 0.2509 (Rfree = 0.000) for 812 atoms. Found 2 (6 requested) and removed 3 (3 requested) atoms. Cycle 40: After refmac, R = 0.2496 (Rfree = 0.000) for 811 atoms. Found 1 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.16 2.72 Search for helices and strands: 0 residues in 0 chains, 828 seeds are put forward Round 1: 62 peptides, 7 chains. Longest chain 19 peptides. Score 0.543 Round 2: 71 peptides, 5 chains. Longest chain 20 peptides. Score 0.683 Round 3: 71 peptides, 7 chains. Longest chain 18 peptides. Score 0.615 Round 4: 69 peptides, 6 chains. Longest chain 19 peptides. Score 0.635 Round 5: 73 peptides, 5 chains. Longest chain 19 peptides. Score 0.695 Taking the results from Round 5 Chains 5, Residues 68, Estimated correctness of the model 56.6 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2552 reflections ( 99.69 % complete ) and 1740 restraints for refining 804 atoms. 1473 conditional restraints added. Observations/parameters ratio is 0.79 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2854 (Rfree = 0.000) for 804 atoms. Found 6 (6 requested) and removed 13 (3 requested) atoms. Cycle 42: After refmac, R = 0.2635 (Rfree = 0.000) for 796 atoms. Found 1 (6 requested) and removed 7 (3 requested) atoms. Cycle 43: After refmac, R = 0.2573 (Rfree = 0.000) for 789 atoms. Found 2 (5 requested) and removed 5 (2 requested) atoms. Cycle 44: After refmac, R = 0.2622 (Rfree = 0.000) for 786 atoms. Found 5 (5 requested) and removed 8 (2 requested) atoms. Cycle 45: After refmac, R = 0.2942 (Rfree = 0.000) for 780 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.18 2.74 Search for helices and strands: 0 residues in 0 chains, 805 seeds are put forward Round 1: 56 peptides, 7 chains. Longest chain 14 peptides. Score 0.489 Round 2: 66 peptides, 9 chains. Longest chain 13 peptides. Score 0.497 Round 3: 74 peptides, 9 chains. Longest chain 17 peptides. Score 0.566 Round 4: 78 peptides, 8 chains. Longest chain 20 peptides. Score 0.631 Round 5: 75 peptides, 6 chains. Longest chain 37 peptides. Score 0.676 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 69, Estimated correctness of the model 51.5 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2od5-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2552 reflections ( 99.69 % complete ) and 1721 restraints for refining 828 atoms. 1451 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3066 (Rfree = 0.000) for 828 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2811 (Rfree = 0.000) for 819 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2933 (Rfree = 0.000) for 814 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.2832 (Rfree = 0.000) for 809 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:47:46 GMT 2018 Job finished. TimeTaking 24.69 Used memory is bytes: 20108712