Sun 23 Dec 22:22:59 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 1vjx-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vjx-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vjx-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjx-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/1vjx-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjx-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 ============================================================ Sun 23 Dec 22:23:08 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/1vjx-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vjx-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 129 and 0 Target number of residues in the AU: 129 Target solvent content: 0.6612 Checking the provided sequence file Detected sequence length: 157 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 157 Adjusted target solvent content: 0.59 Input MTZ file: 1vjx-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: 98 Cell parameters: 82.326 82.326 121.618 90.000 90.000 90.000 Input sequence file: 1vjx-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 1256 target number of atoms Had to go as low as 0.80 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: 68.175 4.001 Wilson plot Bfac: 85.56 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1859 reflections ( 95.97 % complete ) and 0 restraints for refining 1395 atoms. Observations/parameters ratio is 0.33 ------------------------------------------------------ Starting model: R = 0.3673 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3826 (Rfree = 0.000) for 1395 atoms. Found 4 (6 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.37 3.87 Search for helices and strands: 0 residues in 0 chains, 1432 seeds are put forward Round 1: 45 peptides, 8 chains. Longest chain 9 peptides. Score 0.305 Round 2: 60 peptides, 11 chains. Longest chain 8 peptides. Score 0.321 Round 3: 61 peptides, 10 chains. Longest chain 8 peptides. Score 0.368 Round 4: 67 peptides, 11 chains. Longest chain 9 peptides. Score 0.381 Round 5: 62 peptides, 10 chains. Longest chain 10 peptides. Score 0.376 Taking the results from Round 4 Chains 11, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1859 reflections ( 95.97 % complete ) and 2737 restraints for refining 1126 atoms. 2524 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3663 (Rfree = 0.000) for 1126 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 2: After refmac, R = 0.3504 (Rfree = 0.000) for 1102 atoms. Found 4 (5 requested) and removed 2 (2 requested) atoms. Cycle 3: After refmac, R = 0.3619 (Rfree = 0.000) for 1091 atoms. Found 4 (5 requested) and removed 4 (2 requested) atoms. Cycle 4: After refmac, R = 0.3648 (Rfree = 0.000) for 1079 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 5: After refmac, R = 0.3745 (Rfree = 0.000) for 1066 atoms. Found 1 (5 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.96 3.51 Search for helices and strands: 0 residues in 0 chains, 1110 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 8 peptides. Score 0.267 Round 2: 68 peptides, 10 chains. Longest chain 18 peptides. Score 0.424 Round 3: 65 peptides, 10 chains. Longest chain 12 peptides. Score 0.401 Round 4: 68 peptides, 8 chains. Longest chain 21 peptides. Score 0.494 Round 5: 75 peptides, 9 chains. Longest chain 18 peptides. Score 0.510 Taking the results from Round 5 Chains 9, Residues 66, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1859 reflections ( 95.97 % complete ) and 2154 restraints for refining 993 atoms. 1899 conditional restraints added. Observations/parameters ratio is 0.47 ------------------------------------------------------ Cycle 6: After refmac, R = 0.4003 (Rfree = 0.000) for 993 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 7: After refmac, R = 0.3614 (Rfree = 0.000) for 971 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 8: After refmac, R = 0.3918 (Rfree = 0.000) for 954 atoms. Found 2 (4 requested) and removed 6 (2 requested) atoms. Cycle 9: After refmac, R = 0.3731 (Rfree = 0.000) for 936 atoms. Found 3 (4 requested) and removed 6 (2 requested) atoms. Cycle 10: After refmac, R = 0.3872 (Rfree = 0.000) for 923 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.37 3.87 Search for helices and strands: 0 residues in 0 chains, 961 seeds are put forward Round 1: 58 peptides, 12 chains. Longest chain 7 peptides. Score 0.265 Round 2: 73 peptides, 13 chains. Longest chain 13 peptides. Score 0.358 Round 3: 65 peptides, 11 chains. Longest chain 14 peptides. Score 0.364 Round 4: 74 peptides, 11 chains. Longest chain 13 peptides. Score 0.436 Round 5: 67 peptides, 11 chains. Longest chain 11 peptides. Score 0.381 Taking the results from Round 4 Chains 11, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1859 reflections ( 95.97 % complete ) and 2031 restraints for refining 938 atoms. 1790 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 11: After refmac, R = 0.4020 (Rfree = 0.000) for 938 atoms. Found 4 (4 requested) and removed 22 (2 requested) atoms. Cycle 12: After refmac, R = 0.4043 (Rfree = 0.000) for 908 atoms. Found 2 (4 requested) and removed 8 (2 requested) atoms. Cycle 13: After refmac, R = 0.3898 (Rfree = 0.000) for 891 atoms. Found 0 (4 requested) and removed 5 (2 requested) atoms. Cycle 14: After refmac, R = 0.3980 (Rfree = 0.000) for 883 atoms. Found 2 (4 requested) and removed 5 (2 requested) atoms. Cycle 15: After refmac, R = 0.4051 (Rfree = 0.000) for 870 atoms. Found 3 (4 requested) and removed 7 (2 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 4.52 4.00 Search for helices and strands: 0 residues in 0 chains, 908 seeds are put forward Round 1: 41 peptides, 8 chains. Longest chain 7 peptides. Score 0.266 Round 2: 62 peptides, 10 chains. Longest chain 10 peptides. Score 0.376 Round 3: 62 peptides, 10 chains. Longest chain 8 peptides. Score 0.376 Round 4: 67 peptides, 10 chains. Longest chain 12 peptides. Score 0.417 Round 5: 73 peptides, 12 chains. Longest chain 12 peptides. Score 0.394 Taking the results from Round 4 Chains 10, Residues 57, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1859 reflections ( 95.97 % complete ) and 2072 restraints for refining 933 atoms. 1854 conditional restraints added. Observations/parameters ratio is 0.50 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3987 (Rfree = 0.000) for 933 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 17: After refmac, R = 0.3911 (Rfree = 0.000) for 912 atoms. Found 0 (4 requested) and removed 4 (2 requested) atoms. Cycle 18: After refmac, R = 0.4036 (Rfree = 0.000) for 898 atoms. Found 0 (4 requested) and removed 5 (2 requested) atoms. Cycle 19: After refmac, R = 0.3989 (Rfree = 0.000) for 881 atoms. Found 0 (4 requested) and removed 3 (2 requested) atoms. Cycle 20: After refmac, R = 0.4019 (Rfree = 0.000) for 871 atoms. Found 0 (4 requested) and removed 5 (2 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.80 3.37 Search for helices and strands: 0 residues in 0 chains, 912 seeds are put forward Round 1: 60 peptides, 11 chains. Longest chain 8 peptides. Score 0.321 Round 2: 68 peptides, 10 chains. Longest chain 10 peptides. Score 0.424 Round 3: 73 peptides, 10 chains. Longest chain 12 peptides. Score 0.463 Round 4: 72 peptides, 10 chains. Longest chain 15 peptides. Score 0.455 Round 5: 68 peptides, 10 chains. Longest chain 13 peptides. Score 0.424 Taking the results from Round 3 Chains 10, Residues 63, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1859 reflections ( 95.97 % complete ) and 1894 restraints for refining 887 atoms. 1652 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 21: After refmac, R = 0.4143 (Rfree = 0.000) for 887 atoms. Found 4 (4 requested) and removed 26 (2 requested) atoms. Cycle 22: After refmac, R = 0.4016 (Rfree = 0.000) for 856 atoms. Found 4 (4 requested) and removed 5 (2 requested) atoms. Cycle 23: After refmac, R = 0.3942 (Rfree = 0.000) for 845 atoms. Found 4 (4 requested) and removed 8 (2 requested) atoms. Cycle 24: After refmac, R = 0.3963 (Rfree = 0.000) for 830 atoms. Found 2 (3 requested) and removed 3 (1 requested) atoms. Cycle 25: After refmac, R = 0.3855 (Rfree = 0.000) for 817 atoms. Found 0 (3 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.83 3.39 Search for helices and strands: 0 residues in 0 chains, 866 seeds are put forward Round 1: 54 peptides, 10 chains. Longest chain 8 peptides. Score 0.306 Round 2: 64 peptides, 9 chains. Longest chain 18 peptides. Score 0.429 Round 3: 64 peptides, 12 chains. Longest chain 8 peptides. Score 0.318 Round 4: 68 peptides, 12 chains. Longest chain 11 peptides. Score 0.353 Round 5: 63 peptides, 10 chains. Longest chain 12 peptides. Score 0.384 Taking the results from Round 2 Chains 9, Residues 55, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1859 reflections ( 95.97 % complete ) and 1847 restraints for refining 850 atoms. 1636 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 26: After refmac, R = 0.4107 (Rfree = 0.000) for 850 atoms. Found 3 (4 requested) and removed 6 (2 requested) atoms. Cycle 27: After refmac, R = 0.4058 (Rfree = 0.000) for 834 atoms. Found 1 (4 requested) and removed 19 (2 requested) atoms. Cycle 28: After refmac, R = 0.3967 (Rfree = 0.000) for 805 atoms. Found 2 (3 requested) and removed 2 (1 requested) atoms. Cycle 29: After refmac, R = 0.4219 (Rfree = 0.000) for 800 atoms. Found 2 (3 requested) and removed 5 (1 requested) atoms. Cycle 30: After refmac, R = 0.4139 (Rfree = 0.000) for 786 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.65 3.23 Search for helices and strands: 0 residues in 0 chains, 816 seeds are put forward Round 1: 42 peptides, 8 chains. Longest chain 9 peptides. Score 0.276 Round 2: 50 peptides, 10 chains. Longest chain 7 peptides. Score 0.269 Round 3: 51 peptides, 8 chains. Longest chain 13 peptides. Score 0.359 Round 4: 57 peptides, 10 chains. Longest chain 9 peptides. Score 0.333 Round 5: 61 peptides, 12 chains. Longest chain 10 peptides. Score 0.292 Taking the results from Round 3 Chains 8, Residues 43, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1859 reflections ( 95.97 % complete ) and 1855 restraints for refining 822 atoms. 1691 conditional restraints added. Observations/parameters ratio is 0.57 ------------------------------------------------------ Cycle 31: After refmac, R = 0.4202 (Rfree = 0.000) for 822 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 32: After refmac, R = 0.4152 (Rfree = 0.000) for 802 atoms. Found 2 (3 requested) and removed 3 (1 requested) atoms. Cycle 33: After refmac, R = 0.4085 (Rfree = 0.000) for 792 atoms. Found 2 (3 requested) and removed 3 (1 requested) atoms. Cycle 34: After refmac, R = 0.4123 (Rfree = 0.000) for 785 atoms. Found 2 (3 requested) and removed 1 (1 requested) atoms. Cycle 35: After refmac, R = 0.4083 (Rfree = 0.000) for 777 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.65 3.23 Search for helices and strands: 0 residues in 0 chains, 816 seeds are put forward Round 1: 46 peptides, 10 chains. Longest chain 7 peptides. Score 0.230 Round 2: 52 peptides, 10 chains. Longest chain 8 peptides. Score 0.288 Round 3: 59 peptides, 11 chains. Longest chain 8 peptides. Score 0.312 Round 4: 62 peptides, 11 chains. Longest chain 9 peptides. Score 0.339 Round 5: 59 peptides, 11 chains. Longest chain 9 peptides. Score 0.312 Taking the results from Round 4 Chains 11, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1859 reflections ( 95.97 % complete ) and 1715 restraints for refining 788 atoms. 1522 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.4083 (Rfree = 0.000) for 788 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 37: After refmac, R = 0.4071 (Rfree = 0.000) for 779 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 38: After refmac, R = 0.4035 (Rfree = 0.000) for 773 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 39: After refmac, R = 0.4044 (Rfree = 0.000) for 769 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 40: After refmac, R = 0.4019 (Rfree = 0.000) for 763 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.32 Search for helices and strands: 0 residues in 0 chains, 811 seeds are put forward Round 1: 47 peptides, 10 chains. Longest chain 7 peptides. Score 0.240 Round 2: 57 peptides, 9 chains. Longest chain 10 peptides. Score 0.372 Round 3: 60 peptides, 9 chains. Longest chain 11 peptides. Score 0.397 Round 4: 64 peptides, 10 chains. Longest chain 11 peptides. Score 0.392 Round 5: 62 peptides, 10 chains. Longest chain 11 peptides. Score 0.376 Taking the results from Round 3 Chains 9, Residues 51, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1859 reflections ( 95.97 % complete ) and 1710 restraints for refining 780 atoms. 1515 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3980 (Rfree = 0.000) for 780 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 42: After refmac, R = 0.4083 (Rfree = 0.000) for 772 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 43: After refmac, R = 0.4127 (Rfree = 0.000) for 764 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 44: After refmac, R = 0.3917 (Rfree = 0.000) for 755 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 45: After refmac, R = 0.3851 (Rfree = 0.000) for 748 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.85 3.41 Search for helices and strands: 0 residues in 0 chains, 800 seeds are put forward Round 1: 43 peptides, 10 chains. Longest chain 5 peptides. Score 0.199 Round 2: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.267 Round 3: 48 peptides, 10 chains. Longest chain 8 peptides. Score 0.250 Round 4: 58 peptides, 10 chains. Longest chain 10 peptides. Score 0.342 Round 5: 57 peptides, 10 chains. Longest chain 11 peptides. Score 0.333 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 48, 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 1vjx-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1859 reflections ( 95.97 % complete ) and 1726 restraints for refining 797 atoms. 1544 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3940 (Rfree = 0.000) for 797 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 47: After refmac, R = 0.4009 (Rfree = 0.000) for 785 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 48: After refmac, R = 0.3989 (Rfree = 0.000) for 771 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 49: After refmac, R = 0.3906 (Rfree = 0.000) for 759 atoms. TimeTaking 24.42