null Sun 23 Dec 22:22:43 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 2od5-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2od5-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2od5-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-3.2-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/2od5-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-3.2-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 22:22:53 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/2od5-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-3.2-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 112 and 0 Target number of residues in the AU: 112 Target solvent content: 0.6205 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: 2od5-3.2-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: 2od5-3.2-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 3.200 Wilson plot Bfac: 61.39 3039 reflections ( 99.74 % complete ) and 0 restraints for refining 1031 atoms. Observations/parameters ratio is 0.74 ------------------------------------------------------ Starting model: R = 0.3774 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3483 (Rfree = 0.000) for 1031 atoms. Found 9 (9 requested) and removed 21 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.11 2.68 Search for helices and strands: 0 residues in 0 chains, 1054 seeds are put forward Round 1: 65 peptides, 11 chains. Longest chain 12 peptides. Score 0.404 Round 2: 79 peptides, 9 chains. Longest chain 17 peptides. Score 0.604 Round 3: 74 peptides, 9 chains. Longest chain 18 peptides. Score 0.566 Round 4: 70 peptides, 7 chains. Longest chain 17 peptides. Score 0.607 Round 5: 75 peptides, 7 chains. Longest chain 22 peptides. Score 0.644 Taking the results from Round 5 Chains 7, Residues 68, Estimated correctness of the model 52.4 % 1 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3039 reflections ( 99.74 % complete ) and 1598 restraints for refining 847 atoms. 1223 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3345 (Rfree = 0.000) for 847 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 2: After refmac, R = 0.3350 (Rfree = 0.000) for 816 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 3: After refmac, R = 0.3222 (Rfree = 0.000) for 799 atoms. Found 4 (7 requested) and removed 4 (3 requested) atoms. Cycle 4: After refmac, R = 0.3172 (Rfree = 0.000) for 789 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 5: After refmac, R = 0.3062 (Rfree = 0.000) for 786 atoms. Found 2 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.12 2.69 Search for helices and strands: 0 residues in 0 chains, 820 seeds are put forward Round 1: 66 peptides, 5 chains. Longest chain 17 peptides. Score 0.649 Round 2: 72 peptides, 6 chains. Longest chain 18 peptides. Score 0.656 Round 3: 78 peptides, 6 chains. Longest chain 22 peptides. Score 0.695 Round 4: 83 peptides, 7 chains. Longest chain 22 peptides. Score 0.696 Round 5: 82 peptides, 6 chains. Longest chain 35 peptides. Score 0.719 Taking the results from Round 5 Chains 7, Residues 76, Estimated correctness of the model 69.1 % 2 chains (51 residues) have been docked in sequence Building loops using Loopy2018 7 chains (76 residues) following loop building 2 chains (51 residues) in sequence following loop building ------------------------------------------------------ 3039 reflections ( 99.74 % complete ) and 1285 restraints for refining 847 atoms. 758 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3342 (Rfree = 0.000) for 847 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 7: After refmac, R = 0.3296 (Rfree = 0.000) for 824 atoms. Found 7 (7 requested) and removed 17 (3 requested) atoms. Cycle 8: After refmac, R = 0.3113 (Rfree = 0.000) for 805 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 9: After refmac, R = 0.2969 (Rfree = 0.000) for 800 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 10: After refmac, R = 0.3083 (Rfree = 0.000) for 793 atoms. Found 5 (6 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.07 2.65 Search for helices and strands: 0 residues in 0 chains, 818 seeds are put forward Round 1: 71 peptides, 6 chains. Longest chain 18 peptides. Score 0.649 Round 2: 75 peptides, 4 chains. Longest chain 32 peptides. Score 0.737 Round 3: 78 peptides, 4 chains. Longest chain 29 peptides. Score 0.754 Round 4: 77 peptides, 5 chains. Longest chain 35 peptides. Score 0.719 Round 5: 79 peptides, 3 chains. Longest chain 35 peptides. Score 0.785 Taking the results from Round 5 Chains 4, Residues 76, Estimated correctness of the model 81.1 % 2 chains (49 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 69 A and 77 A 3 chains (83 residues) following loop building 1 chains (56 residues) in sequence following loop building ------------------------------------------------------ 3039 reflections ( 99.74 % complete ) and 1149 restraints for refining 847 atoms. 593 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3064 (Rfree = 0.000) for 847 atoms. Found 6 (6 requested) and removed 14 (3 requested) atoms. Cycle 12: After refmac, R = 0.2719 (Rfree = 0.000) for 832 atoms. Found 4 (6 requested) and removed 9 (3 requested) atoms. Cycle 13: After refmac, R = 0.2808 (Rfree = 0.000) for 824 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. Cycle 14: After refmac, R = 0.2396 (Rfree = 0.000) for 817 atoms. Found 3 (6 requested) and removed 6 (3 requested) atoms. Cycle 15: After refmac, R = 0.2338 (Rfree = 0.000) for 807 atoms. Found 5 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.08 2.65 Search for helices and strands: 0 residues in 0 chains, 836 seeds are put forward Round 1: 77 peptides, 4 chains. Longest chain 32 peptides. Score 0.748 Round 2: 80 peptides, 4 chains. Longest chain 40 peptides. Score 0.764 Round 3: 85 peptides, 2 chains. Longest chain 63 peptides. Score 0.834 Round 4: 83 peptides, 4 chains. Longest chain 32 peptides. Score 0.779 Round 5: 88 peptides, 4 chains. Longest chain 54 peptides. Score 0.801 Taking the results from Round 3 Chains 4, Residues 83, Estimated correctness of the model 88.2 % 2 chains (78 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 77 A 2 chains (87 residues) following loop building 1 chains (83 residues) in sequence following loop building ------------------------------------------------------ 3039 reflections ( 99.74 % complete ) and 878 restraints for refining 847 atoms. 189 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2596 (Rfree = 0.000) for 847 atoms. Found 6 (6 requested) and removed 24 (3 requested) atoms. Cycle 17: After refmac, R = 0.2380 (Rfree = 0.000) for 821 atoms. Found 3 (5 requested) and removed 7 (3 requested) atoms. Cycle 18: After refmac, R = 0.2244 (Rfree = 0.000) for 813 atoms. Found 3 (5 requested) and removed 6 (3 requested) atoms. Cycle 19: After refmac, R = 0.2228 (Rfree = 0.000) for 805 atoms. Found 5 (5 requested) and removed 4 (3 requested) atoms. Cycle 20: After refmac, R = 0.2203 (Rfree = 0.000) for 803 atoms. Found 3 (5 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.09 2.66 Search for helices and strands: 0 residues in 0 chains, 816 seeds are put forward Round 1: 79 peptides, 3 chains. Longest chain 33 peptides. Score 0.785 Round 2: 83 peptides, 2 chains. Longest chain 64 peptides. Score 0.827 Round 3: 86 peptides, 5 chains. Longest chain 35 peptides. Score 0.768 Round 4: 82 peptides, 4 chains. Longest chain 40 peptides. Score 0.774 Round 5: 77 peptides, 5 chains. Longest chain 22 peptides. Score 0.719 Taking the results from Round 2 Chains 4, Residues 81, Estimated correctness of the model 87.3 % 2 chains (79 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 72 A and 77 A 2 chains (84 residues) following loop building 2 chains (84 residues) in sequence following loop building ------------------------------------------------------ 3039 reflections ( 99.74 % complete ) and 865 restraints for refining 843 atoms. 188 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2553 (Rfree = 0.000) for 843 atoms. Found 4 (5 requested) and removed 27 (3 requested) atoms. Cycle 22: After refmac, R = 0.2254 (Rfree = 0.000) for 813 atoms. Found 5 (5 requested) and removed 5 (3 requested) atoms. Cycle 23: After refmac, R = 0.2145 (Rfree = 0.000) for 805 atoms. Found 1 (5 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.2162 (Rfree = 0.000) for 799 atoms. Found 1 (4 requested) and removed 3 (3 requested) atoms. Cycle 25: After refmac, R = 0.2275 (Rfree = 0.000) for 794 atoms. Found 4 (4 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.10 2.67 Search for helices and strands: 0 residues in 0 chains, 817 seeds are put forward Round 1: 79 peptides, 4 chains. Longest chain 33 peptides. Score 0.759 Round 2: 82 peptides, 4 chains. Longest chain 32 peptides. Score 0.774 Round 3: 83 peptides, 4 chains. Longest chain 54 peptides. Score 0.779 Round 4: 80 peptides, 3 chains. Longest chain 51 peptides. Score 0.790 Round 5: 79 peptides, 3 chains. Longest chain 48 peptides. Score 0.785 Taking the results from Round 4 Chains 5, Residues 77, Estimated correctness of the model 81.9 % 2 chains (62 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 70 A and 80 A 3 chains (79 residues) following loop building 1 chains (71 residues) in sequence following loop building ------------------------------------------------------ 3039 reflections ( 99.74 % complete ) and 989 restraints for refining 839 atoms. 384 conditional restraints added. Observations/parameters ratio is 0.91 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2721 (Rfree = 0.000) for 839 atoms. Found 4 (4 requested) and removed 17 (3 requested) atoms. Cycle 27: After refmac, R = 0.2522 (Rfree = 0.000) for 818 atoms. Found 4 (4 requested) and removed 6 (3 requested) atoms. Cycle 28: After refmac, R = 0.2544 (Rfree = 0.000) for 811 atoms. Found 4 (4 requested) and removed 9 (3 requested) atoms. Cycle 29: After refmac, R = 0.2132 (Rfree = 0.000) for 800 atoms. Found 4 (4 requested) and removed 3 (3 requested) atoms. Cycle 30: After refmac, R = 0.2085 (Rfree = 0.000) for 794 atoms. Found 1 (4 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.14 2.71 Search for helices and strands: 0 residues in 0 chains, 818 seeds are put forward Round 1: 77 peptides, 5 chains. Longest chain 25 peptides. Score 0.719 Round 2: 83 peptides, 4 chains. Longest chain 54 peptides. Score 0.779 Round 3: 79 peptides, 3 chains. Longest chain 55 peptides. Score 0.785 Round 4: 74 peptides, 6 chains. Longest chain 20 peptides. Score 0.670 Round 5: 77 peptides, 5 chains. Longest chain 21 peptides. Score 0.719 Taking the results from Round 3 Chains 3, Residues 76, Estimated correctness of the model 81.1 % 2 chains (72 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 32 A and 41 A 2 chains (84 residues) following loop building 1 chains (80 residues) in sequence following loop building ------------------------------------------------------ 3039 reflections ( 99.74 % complete ) and 877 restraints for refining 847 atoms. 208 conditional restraints added. Observations/parameters ratio is 0.90 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2686 (Rfree = 0.000) for 847 atoms. Found 3 (3 requested) and removed 22 (3 requested) atoms. Cycle 32: After refmac, R = 0.2314 (Rfree = 0.000) for 822 atoms. Found 3 (3 requested) and removed 5 (3 requested) atoms. Cycle 33: After refmac, R = 0.2246 (Rfree = 0.000) for 815 atoms. Found 3 (3 requested) and removed 4 (3 requested) atoms. Cycle 34: After refmac, R = 0.2027 (Rfree = 0.000) for 805 atoms. Found 3 (3 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.1937 (Rfree = 0.000) for 802 atoms. Found 3 (3 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.15 2.71 Search for helices and strands: 0 residues in 0 chains, 834 seeds are put forward Round 1: 76 peptides, 6 chains. Longest chain 23 peptides. Score 0.683 Round 2: 77 peptides, 3 chains. Longest chain 55 peptides. Score 0.776 Round 3: 84 peptides, 5 chains. Longest chain 33 peptides. Score 0.758 Round 4: 82 peptides, 5 chains. Longest chain 38 peptides. Score 0.747 Round 5: 82 peptides, 6 chains. Longest chain 34 peptides. Score 0.719 Taking the results from Round 2 Chains 3, Residues 74, Estimated correctness of the model 79.6 % 2 chains (67 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 34 A and 39 A 2 chains (78 residues) following loop building 1 chains (71 residues) in sequence following loop building ------------------------------------------------------ 3039 reflections ( 99.74 % complete ) and 1019 restraints for refining 831 atoms. 420 conditional restraints added. Observations/parameters ratio is 0.91 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2731 (Rfree = 0.000) for 831 atoms. Found 3 (3 requested) and removed 13 (3 requested) atoms. Cycle 37: After refmac, R = 0.2663 (Rfree = 0.000) for 817 atoms. Found 3 (3 requested) and removed 6 (3 requested) atoms. Cycle 38: After refmac, R = 0.2720 (Rfree = 0.000) for 804 atoms. Found 3 (3 requested) and removed 8 (3 requested) atoms. Cycle 39: After refmac, R = 0.2258 (Rfree = 0.000) for 795 atoms. Found 3 (3 requested) and removed 6 (3 requested) atoms. Cycle 40: After refmac, R = 0.2186 (Rfree = 0.000) for 789 atoms. Found 3 (3 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.11 2.68 Search for helices and strands: 0 residues in 0 chains, 821 seeds are put forward Round 1: 79 peptides, 5 chains. Longest chain 51 peptides. Score 0.731 Round 2: 75 peptides, 4 chains. Longest chain 37 peptides. Score 0.737 Round 3: 77 peptides, 3 chains. Longest chain 60 peptides. Score 0.776 Round 4: 79 peptides, 5 chains. Longest chain 24 peptides. Score 0.731 Round 5: 80 peptides, 4 chains. Longest chain 48 peptides. Score 0.764 Taking the results from Round 3 Chains 3, Residues 74, Estimated correctness of the model 79.6 % 1 chains (59 residues) have been docked in sequence ------------------------------------------------------ 3039 reflections ( 99.74 % complete ) and 1130 restraints for refining 814 atoms. 599 conditional restraints added. Observations/parameters ratio is 0.93 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2936 (Rfree = 0.000) for 814 atoms. Found 3 (3 requested) and removed 16 (3 requested) atoms. Cycle 42: After refmac, R = 0.2495 (Rfree = 0.000) for 794 atoms. Found 3 (3 requested) and removed 5 (3 requested) atoms. Cycle 43: After refmac, R = 0.2424 (Rfree = 0.000) for 788 atoms. Found 3 (3 requested) and removed 6 (3 requested) atoms. Cycle 44: After refmac, R = 0.2393 (Rfree = 0.000) for 780 atoms. Found 3 (3 requested) and removed 5 (3 requested) atoms. Cycle 45: After refmac, R = 0.2375 (Rfree = 0.000) for 774 atoms. Found 3 (3 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.09 2.66 Search for helices and strands: 0 residues in 0 chains, 799 seeds are put forward Round 1: 79 peptides, 6 chains. Longest chain 37 peptides. Score 0.701 Round 2: 77 peptides, 4 chains. Longest chain 43 peptides. Score 0.748 Round 3: 82 peptides, 4 chains. Longest chain 41 peptides. Score 0.774 Round 4: 81 peptides, 5 chains. Longest chain 39 peptides. Score 0.742 Round 5: 78 peptides, 4 chains. Longest chain 44 peptides. Score 0.754 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 8, Residues 78, Estimated correctness of the model 79.3 % 2 chains (53 residues) have been docked in sequence Sequence coverage is 67 % Consider running further cycles of model building using 2od5-3_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 70 A and 77 A 5 chains (80 residues) following loop building 1 chains (59 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3039 reflections ( 99.74 % complete ) and 1013 restraints for refining 799 atoms. 461 conditional restraints added. Observations/parameters ratio is 0.95 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2660 (Rfree = 0.000) for 799 atoms. Found 0 (3 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.2660 (Rfree = 0.000) for 787 atoms. Found 0 (3 requested) and removed 1 (3 requested) atoms. Cycle 48: After refmac, R = 0.2246 (Rfree = 0.000) for 783 atoms. Found 0 (3 requested) and removed 2 (3 requested) atoms. Cycle 49: After refmac, R = 0.2276 (Rfree = 0.000) for 777 atoms. Found 0 (3 requested) and removed 2 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:49:16 GMT 2018 Job finished. TimeTaking 26.54 Used memory is bytes: 17695024