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 1vku-1.9-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vku-1.9-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vku-1.9-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-1.9-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/1vku-1.9-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-1.9-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/1vku-1.9-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vku-1.9-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 84 and 0 Target number of residues in the AU: 84 Target solvent content: 0.4872 Checking the provided sequence file Detected sequence length: 100 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 100 Adjusted target solvent content: 0.39 Input MTZ file: 1vku-1.9-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: 154 Cell parameters: 45.440 45.440 74.373 90.000 90.000 120.000 Input sequence file: 1vku-1.9-parrot-hancs.fasta_lf Building free atoms model in initial map for 800 target number of atoms Had to go as low as 0.40 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 1 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: 39.352 1.940 Wilson plot Bfac: 20.22 6577 reflections ( 94.54 % complete ) and 0 restraints for refining 887 atoms. Observations/parameters ratio is 1.85 ------------------------------------------------------ Starting model: R = 0.3262 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2710 (Rfree = 0.000) for 887 atoms. Found 21 (33 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.03 2.36 Round 1: 69 peptides, 11 chains. Longest chain 10 peptides. Score 0.590 Round 2: 80 peptides, 4 chains. Longest chain 30 peptides. Score 0.910 Round 3: 81 peptides, 2 chains. Longest chain 56 peptides. Score 0.947 Round 4: 81 peptides, 3 chains. Longest chain 64 peptides. Score 0.931 Round 5: 83 peptides, 2 chains. Longest chain 59 peptides. Score 0.950 Taking the results from Round 5 Chains 3, Residues 81, Estimated correctness of the model 99.7 % 2 chains (80 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 33 A and 36 A 2 chains (83 residues) following loop building 2 chains (83 residues) in sequence following loop building ------------------------------------------------------ 6577 reflections ( 94.54 % complete ) and 728 restraints for refining 779 atoms. 40 conditional restraints added. Observations/parameters ratio is 2.11 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2849 (Rfree = 0.000) for 779 atoms. Found 29 (29 requested) and removed 16 (14 requested) atoms. Cycle 2: After refmac, R = 0.2745 (Rfree = 0.000) for 781 atoms. Found 25 (28 requested) and removed 14 (14 requested) atoms. Cycle 3: After refmac, R = 0.2616 (Rfree = 0.000) for 791 atoms. Found 19 (28 requested) and removed 5 (14 requested) atoms. Cycle 4: After refmac, R = 0.2522 (Rfree = 0.000) for 802 atoms. Found 12 (29 requested) and removed 6 (15 requested) atoms. Cycle 5: After refmac, R = 0.2444 (Rfree = 0.000) for 802 atoms. Found 11 (29 requested) and removed 3 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.03 2.36 Round 1: 81 peptides, 2 chains. Longest chain 58 peptides. Score 0.947 Round 2: 83 peptides, 1 chains. Longest chain 83 peptides. Score 0.964 Round 3: 82 peptides, 2 chains. Longest chain 59 peptides. Score 0.949 Round 4: 84 peptides, 1 chains. Longest chain 84 peptides. Score 0.966 Round 5: 82 peptides, 2 chains. Longest chain 58 peptides. Score 0.949 Taking the results from Round 4 Chains 1, Residues 83, Estimated correctness of the model 99.9 % 1 chains (83 residues) have been docked in sequence ------------------------------------------------------ 6577 reflections ( 94.54 % complete ) and 736 restraints for refining 787 atoms. 40 conditional restraints added. Observations/parameters ratio is 2.09 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2600 (Rfree = 0.000) for 787 atoms. Found 26 (28 requested) and removed 14 (14 requested) atoms. Cycle 7: After refmac, R = 0.2517 (Rfree = 0.000) for 797 atoms. Found 16 (27 requested) and removed 14 (14 requested) atoms. Cycle 8: After refmac, R = 0.2427 (Rfree = 0.000) for 798 atoms. Found 20 (27 requested) and removed 13 (14 requested) atoms. Cycle 9: After refmac, R = 0.2363 (Rfree = 0.000) for 804 atoms. Found 11 (27 requested) and removed 4 (15 requested) atoms. Cycle 10: After refmac, R = 0.2362 (Rfree = 0.000) for 808 atoms. Found 14 (27 requested) and removed 5 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.01 2.33 Round 1: 79 peptides, 2 chains. Longest chain 55 peptides. Score 0.943 Round 2: 83 peptides, 2 chains. Longest chain 56 peptides. Score 0.950 Round 3: 84 peptides, 1 chains. Longest chain 84 peptides. Score 0.966 Round 4: 83 peptides, 2 chains. Longest chain 55 peptides. Score 0.950 Round 5: 84 peptides, 1 chains. Longest chain 84 peptides. Score 0.966 Taking the results from Round 5 Chains 1, Residues 83, Estimated correctness of the model 99.9 % 1 chains (83 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6577 reflections ( 94.54 % complete ) and 738 restraints for refining 785 atoms. 42 conditional restraints added. Observations/parameters ratio is 2.09 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2544 (Rfree = 0.000) for 785 atoms. Found 26 (26 requested) and removed 14 (14 requested) atoms. Cycle 12: After refmac, R = 0.2465 (Rfree = 0.000) for 797 atoms. Found 24 (26 requested) and removed 14 (14 requested) atoms. Cycle 13: After refmac, R = 0.2423 (Rfree = 0.000) for 805 atoms. Found 19 (26 requested) and removed 16 (15 requested) atoms. Cycle 14: After refmac, R = 0.2334 (Rfree = 0.000) for 807 atoms. Found 21 (25 requested) and removed 12 (15 requested) atoms. Cycle 15: After refmac, R = 0.2326 (Rfree = 0.000) for 815 atoms. Found 22 (25 requested) and removed 14 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.01 2.33 Round 1: 82 peptides, 2 chains. Longest chain 55 peptides. Score 0.949 Round 2: 83 peptides, 2 chains. Longest chain 56 peptides. Score 0.950 Round 3: 83 peptides, 2 chains. Longest chain 77 peptides. Score 0.950 Round 4: 84 peptides, 1 chains. Longest chain 84 peptides. Score 0.966 Round 5: 84 peptides, 1 chains. Longest chain 84 peptides. Score 0.966 Taking the results from Round 5 Chains 1, Residues 83, Estimated correctness of the model 99.9 % 1 chains (83 residues) have been docked in sequence ------------------------------------------------------ 6577 reflections ( 94.54 % complete ) and 738 restraints for refining 794 atoms. 42 conditional restraints added. Observations/parameters ratio is 2.07 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2526 (Rfree = 0.000) for 794 atoms. Found 23 (23 requested) and removed 15 (14 requested) atoms. Cycle 17: After refmac, R = 0.2366 (Rfree = 0.000) for 802 atoms. Found 19 (23 requested) and removed 14 (14 requested) atoms. Cycle 18: After refmac, R = 0.2287 (Rfree = 0.000) for 807 atoms. Found 18 (23 requested) and removed 10 (15 requested) atoms. Cycle 19: After refmac, R = 0.2265 (Rfree = 0.000) for 814 atoms. Found 18 (22 requested) and removed 9 (15 requested) atoms. Cycle 20: After refmac, R = 0.2227 (Rfree = 0.000) for 823 atoms. Found 14 (22 requested) and removed 7 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.02 2.34 Round 1: 84 peptides, 1 chains. Longest chain 84 peptides. Score 0.966 Round 2: 83 peptides, 2 chains. Longest chain 47 peptides. Score 0.950 Round 3: 83 peptides, 2 chains. Longest chain 77 peptides. Score 0.950 Round 4: 83 peptides, 2 chains. Longest chain 58 peptides. Score 0.950 Round 5: 84 peptides, 1 chains. Longest chain 84 peptides. Score 0.966 Taking the results from Round 5 Chains 1, Residues 83, Estimated correctness of the model 99.9 % 1 chains (83 residues) have been docked in sequence ------------------------------------------------------ 6577 reflections ( 94.54 % complete ) and 746 restraints for refining 800 atoms. 50 conditional restraints added. Observations/parameters ratio is 2.06 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2457 (Rfree = 0.000) for 800 atoms. Found 21 (21 requested) and removed 15 (14 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.2307 (Rfree = 0.000) for 806 atoms. Found 22 (22 requested) and removed 10 (15 requested) atoms. Cycle 23: After refmac, R = 0.2244 (Rfree = 0.000) for 818 atoms. Found 13 (22 requested) and removed 13 (15 requested) atoms. Cycle 24: After refmac, R = 0.2214 (Rfree = 0.000) for 816 atoms. Found 16 (21 requested) and removed 7 (15 requested) atoms. Cycle 25: After refmac, R = 0.2165 (Rfree = 0.000) for 825 atoms. Found 16 (21 requested) and removed 7 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.01 2.33 Round 1: 81 peptides, 2 chains. Longest chain 59 peptides. Score 0.947 Round 2: 83 peptides, 1 chains. Longest chain 83 peptides. Score 0.964 Round 3: 82 peptides, 2 chains. Longest chain 68 peptides. Score 0.949 Round 4: 82 peptides, 2 chains. Longest chain 68 peptides. Score 0.949 Round 5: 81 peptides, 3 chains. Longest chain 68 peptides. Score 0.931 Taking the results from Round 2 Chains 1, Residues 82, Estimated correctness of the model 99.9 % 1 chains (82 residues) have been docked in sequence ------------------------------------------------------ 6577 reflections ( 94.54 % complete ) and 754 restraints for refining 807 atoms. 69 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2389 (Rfree = 0.000) for 807 atoms. Found 19 (21 requested) and removed 17 (15 requested) atoms. Failed to save intermediate PDB Cycle 27: After refmac, R = 0.2269 (Rfree = 0.000) for 808 atoms. Found 16 (20 requested) and removed 7 (15 requested) atoms. Cycle 28: After refmac, R = 0.2195 (Rfree = 0.000) for 814 atoms. Found 17 (20 requested) and removed 7 (15 requested) atoms. Cycle 29: After refmac, R = 0.2166 (Rfree = 0.000) for 824 atoms. Found 17 (20 requested) and removed 7 (15 requested) atoms. Failed to save intermediate PDB Cycle 30: After refmac, R = 0.2147 (Rfree = 0.000) for 829 atoms. Found 19 (21 requested) and removed 15 (15 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.00 2.32 Round 1: 83 peptides, 1 chains. Longest chain 83 peptides. Score 0.964 Round 2: 82 peptides, 2 chains. Longest chain 55 peptides. Score 0.949 Round 3: 81 peptides, 3 chains. Longest chain 41 peptides. Score 0.931 Round 4: 75 peptides, 2 chains. Longest chain 51 peptides. Score 0.933 Round 5: 79 peptides, 1 chains. Longest chain 79 peptides. Score 0.958 Taking the results from Round 1 Chains 1, Residues 82, Estimated correctness of the model 99.9 % 1 chains (82 residues) have been docked in sequence ------------------------------------------------------ 6577 reflections ( 94.54 % complete ) and 749 restraints for refining 803 atoms. 64 conditional restraints added. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2340 (Rfree = 0.000) for 803 atoms. Found 20 (20 requested) and removed 17 (15 requested) atoms. Failed to save intermediate PDB Cycle 32: After refmac, R = 0.2227 (Rfree = 0.000) for 805 atoms. Found 17 (19 requested) and removed 4 (15 requested) atoms. Cycle 33: After refmac, R = 0.2137 (Rfree = 0.000) for 817 atoms. Found 12 (19 requested) and removed 5 (15 requested) atoms. Cycle 34: After refmac, R = 0.2096 (Rfree = 0.000) for 821 atoms. Found 15 (19 requested) and removed 4 (15 requested) atoms. Cycle 35: After refmac, R = 0.2047 (Rfree = 0.000) for 832 atoms. Found 14 (20 requested) and removed 13 (15 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.01 2.33 Round 1: 80 peptides, 2 chains. Longest chain 58 peptides. Score 0.945 Round 2: 82 peptides, 2 chains. Longest chain 59 peptides. Score 0.949 Round 3: 83 peptides, 1 chains. Longest chain 83 peptides. Score 0.964 Round 4: 81 peptides, 1 chains. Longest chain 81 peptides. Score 0.961 Round 5: 82 peptides, 2 chains. Longest chain 68 peptides. Score 0.949 Taking the results from Round 3 Chains 1, Residues 82, Estimated correctness of the model 99.9 % 1 chains (82 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 6577 reflections ( 94.54 % complete ) and 751 restraints for refining 799 atoms. 66 conditional restraints added. Observations/parameters ratio is 2.06 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2319 (Rfree = 0.000) for 799 atoms. Found 18 (18 requested) and removed 17 (14 requested) atoms. Cycle 37: After refmac, R = 0.2186 (Rfree = 0.000) for 796 atoms. Found 17 (17 requested) and removed 3 (14 requested) atoms. Cycle 38: After refmac, R = 0.2158 (Rfree = 0.000) for 808 atoms. Found 18 (18 requested) and removed 9 (15 requested) atoms. Failed to save intermediate PDB Cycle 39: After refmac, R = 0.2121 (Rfree = 0.000) for 815 atoms. Found 15 (18 requested) and removed 10 (15 requested) atoms. Cycle 40: After refmac, R = 0.2082 (Rfree = 0.000) for 820 atoms. Found 12 (17 requested) and removed 9 (15 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.02 2.34 Round 1: 80 peptides, 2 chains. Longest chain 58 peptides. Score 0.945 Round 2: 82 peptides, 1 chains. Longest chain 82 peptides. Score 0.963 Round 3: 79 peptides, 2 chains. Longest chain 57 peptides. Score 0.943 Round 4: 80 peptides, 2 chains. Longest chain 57 peptides. Score 0.945 Round 5: 81 peptides, 2 chains. Longest chain 57 peptides. Score 0.947 Taking the results from Round 2 Chains 1, Residues 81, Estimated correctness of the model 99.8 % 1 chains (81 residues) have been docked in sequence ------------------------------------------------------ 6577 reflections ( 94.54 % complete ) and 739 restraints for refining 790 atoms. 62 conditional restraints added. Observations/parameters ratio is 2.08 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2326 (Rfree = 0.000) for 790 atoms. Found 16 (16 requested) and removed 11 (14 requested) atoms. Cycle 42: After refmac, R = 0.2236 (Rfree = 0.000) for 792 atoms. Found 14 (16 requested) and removed 3 (14 requested) atoms. Cycle 43: After refmac, R = 0.2164 (Rfree = 0.000) for 802 atoms. Found 14 (16 requested) and removed 7 (15 requested) atoms. Cycle 44: After refmac, R = 0.2113 (Rfree = 0.000) for 808 atoms. Found 12 (16 requested) and removed 8 (15 requested) atoms. Cycle 45: After refmac, R = 0.2052 (Rfree = 0.000) for 812 atoms. Found 16 (16 requested) and removed 8 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.02 2.34 Round 1: 82 peptides, 2 chains. Longest chain 58 peptides. Score 0.949 Round 2: 82 peptides, 2 chains. Longest chain 58 peptides. Score 0.949 Round 3: 83 peptides, 1 chains. Longest chain 83 peptides. Score 0.964 Round 4: 82 peptides, 2 chains. Longest chain 69 peptides. Score 0.949 Round 5: 82 peptides, 2 chains. Longest chain 58 peptides. Score 0.949 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 1, Residues 82, Estimated correctness of the model 99.9 % 1 chains (82 residues) have been docked in sequence Sequence coverage is 98 % All DUM atoms will be removed ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 6577 reflections ( 94.54 % complete ) and 688 restraints for refining 681 atoms. Observations/parameters ratio is 2.41 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2638 (Rfree = 0.000) for 681 atoms. Found 2 (13 requested) and removed 0 (13 requested) atoms. Failed to save intermediate PDB Cycle 47: After refmac, R = 0.2498 (Rfree = 0.000) for 681 atoms. Found 0 (13 requested) and removed 0 (12 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2428 (Rfree = 0.000) for 681 atoms. Found 0 (13 requested) and removed 1 (12 requested) atoms. Cycle 49: After refmac, R = 0.2383 (Rfree = 0.000) for 681 atoms. Found 0 (12 requested) and removed 0 (12 requested) atoms. Writing output files ... Failed to save intermediate PDB Normal termination of warpNtrace Tue 25 Dec 19:56:38 GMT 2018 Job finished. TimeTaking 28.68