Sun 23 Dec 22:22:46 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 2pv4-3.4-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2pv4-3.4-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2pv4-3.4-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-3.4-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/2pv4-3.4-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-3.4-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 22:22:56 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/2pv4-3.4-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2pv4-3.4-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 108 and 0 Target number of residues in the AU: 108 Target solvent content: 0.6517 Checking the provided sequence file Detected sequence length: 145 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 145 Adjusted target solvent content: 0.53 Input MTZ file: 2pv4-3.4-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: 19 Cell parameters: 35.957 47.283 98.695 90.000 90.000 90.000 Input sequence file: 2pv4-3.4-parrot-hancs.fasta_lf Building free atoms model in initial map for 1160 target number of atoms Had to go as low as 0.70 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: 49.347 3.401 Wilson plot Bfac: 77.99 2543 reflections ( 99.45 % complete ) and 0 restraints for refining 1284 atoms. Observations/parameters ratio is 0.50 ------------------------------------------------------ Starting model: R = 0.3369 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3591 (Rfree = 0.000) for 1284 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 3.31 Search for helices and strands: 0 residues in 0 chains, 1321 seeds are put forward Round 1: 54 peptides, 11 chains. Longest chain 7 peptides. Score 0.283 Round 2: 76 peptides, 13 chains. Longest chain 9 peptides. Score 0.418 Round 3: 80 peptides, 12 chains. Longest chain 10 peptides. Score 0.492 Round 4: 80 peptides, 11 chains. Longest chain 15 peptides. Score 0.529 Round 5: 86 peptides, 12 chains. Longest chain 13 peptides. Score 0.542 Taking the results from Round 5 Chains 12, Residues 74, Estimated correctness of the model 8.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2543 reflections ( 99.45 % complete ) and 2319 restraints for refining 1041 atoms. 2035 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3519 (Rfree = 0.000) for 1041 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 2: After refmac, R = 0.3411 (Rfree = 0.000) for 1022 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 3: After refmac, R = 0.3325 (Rfree = 0.000) for 1008 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 4: After refmac, R = 0.3286 (Rfree = 0.000) for 988 atoms. Found 7 (7 requested) and removed 18 (3 requested) atoms. Cycle 5: After refmac, R = 0.3350 (Rfree = 0.000) for 972 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.43 3.30 Search for helices and strands: 0 residues in 0 chains, 1045 seeds are put forward Round 1: 59 peptides, 12 chains. Longest chain 8 peptides. Score 0.291 Round 2: 67 peptides, 11 chains. Longest chain 10 peptides. Score 0.415 Round 3: 72 peptides, 10 chains. Longest chain 14 peptides. Score 0.500 Round 4: 70 peptides, 9 chains. Longest chain 13 peptides. Score 0.521 Round 5: 79 peptides, 10 chains. Longest chain 13 peptides. Score 0.557 Taking the results from Round 5 Chains 10, Residues 69, Estimated correctness of the model 13.9 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2543 reflections ( 99.45 % complete ) and 2105 restraints for refining 1000 atoms. 1802 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3485 (Rfree = 0.000) for 1000 atoms. Found 7 (7 requested) and removed 15 (3 requested) atoms. Cycle 7: After refmac, R = 0.3407 (Rfree = 0.000) for 974 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 8: After refmac, R = 0.3284 (Rfree = 0.000) for 961 atoms. Found 7 (7 requested) and removed 7 (3 requested) atoms. Cycle 9: After refmac, R = 0.3470 (Rfree = 0.000) for 953 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. Cycle 10: After refmac, R = 0.3428 (Rfree = 0.000) for 943 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.45 3.31 Search for helices and strands: 0 residues in 0 chains, 1018 seeds are put forward Round 1: 65 peptides, 13 chains. Longest chain 11 peptides. Score 0.310 Round 2: 79 peptides, 13 chains. Longest chain 13 peptides. Score 0.446 Round 3: 83 peptides, 14 chains. Longest chain 9 peptides. Score 0.443 Round 4: 86 peptides, 13 chains. Longest chain 9 peptides. Score 0.506 Round 5: 83 peptides, 11 chains. Longest chain 15 peptides. Score 0.553 Taking the results from Round 5 Chains 11, Residues 72, Estimated correctness of the model 12.5 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2543 reflections ( 99.45 % complete ) and 2160 restraints for refining 1006 atoms. 1883 conditional restraints added. Observations/parameters ratio is 0.63 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3416 (Rfree = 0.000) for 1006 atoms. Found 7 (7 requested) and removed 11 (3 requested) atoms. Cycle 12: After refmac, R = 0.3278 (Rfree = 0.000) for 989 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 13: After refmac, R = 0.3362 (Rfree = 0.000) for 979 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 14: After refmac, R = 0.3440 (Rfree = 0.000) for 964 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 15: After refmac, R = 0.3226 (Rfree = 0.000) for 964 atoms. Found 7 (7 requested) and removed 5 (3 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.49 3.35 Search for helices and strands: 0 residues in 0 chains, 1033 seeds are put forward Round 1: 67 peptides, 13 chains. Longest chain 12 peptides. Score 0.331 Round 2: 86 peptides, 14 chains. Longest chain 12 peptides. Score 0.469 Round 3: 74 peptides, 13 chains. Longest chain 10 peptides. Score 0.399 Round 4: 85 peptides, 15 chains. Longest chain 9 peptides. Score 0.422 Round 5: 81 peptides, 14 chains. Longest chain 10 peptides. Score 0.425 Taking the results from Round 2 Chains 14, Residues 72, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2543 reflections ( 99.45 % complete ) and 2028 restraints for refining 948 atoms. 1754 conditional restraints added. Observations/parameters ratio is 0.67 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3277 (Rfree = 0.000) for 948 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 17: After refmac, R = 0.3369 (Rfree = 0.000) for 943 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 18: After refmac, R = 0.3092 (Rfree = 0.000) for 937 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 19: After refmac, R = 0.3285 (Rfree = 0.000) for 931 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. Cycle 20: After refmac, R = 0.3006 (Rfree = 0.000) for 930 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.34 Search for helices and strands: 0 residues in 0 chains, 999 seeds are put forward Round 1: 53 peptides, 11 chains. Longest chain 6 peptides. Score 0.272 Round 2: 64 peptides, 11 chains. Longest chain 11 peptides. Score 0.386 Round 3: 66 peptides, 11 chains. Longest chain 10 peptides. Score 0.405 Round 4: 70 peptides, 9 chains. Longest chain 11 peptides. Score 0.521 Round 5: 76 peptides, 11 chains. Longest chain 11 peptides. Score 0.496 Taking the results from Round 4 Chains 9, Residues 61, Estimated correctness of the model 0.7 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2543 reflections ( 99.45 % complete ) and 2032 restraints for refining 937 atoms. 1797 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3453 (Rfree = 0.000) for 937 atoms. Found 7 (7 requested) and removed 14 (3 requested) atoms. Cycle 22: After refmac, R = 0.3473 (Rfree = 0.000) for 922 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 23: After refmac, R = 0.3565 (Rfree = 0.000) for 912 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 24: After refmac, R = 0.3366 (Rfree = 0.000) for 910 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 25: After refmac, R = 0.3767 (Rfree = 0.000) for 907 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 967 seeds are put forward Round 1: 60 peptides, 12 chains. Longest chain 9 peptides. Score 0.302 Round 2: 64 peptides, 11 chains. Longest chain 11 peptides. Score 0.386 Round 3: 57 peptides, 10 chains. Longest chain 7 peptides. Score 0.359 Round 4: 65 peptides, 12 chains. Longest chain 8 peptides. Score 0.353 Round 5: 62 peptides, 11 chains. Longest chain 7 peptides. Score 0.366 Taking the results from Round 2 Chains 11, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2543 reflections ( 99.45 % complete ) and 1874 restraints for refining 896 atoms. 1673 conditional restraints added. Observations/parameters ratio is 0.71 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3418 (Rfree = 0.000) for 896 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 27: After refmac, R = 0.3330 (Rfree = 0.000) for 889 atoms. Found 6 (6 requested) and removed 4 (3 requested) atoms. Cycle 28: After refmac, R = 0.3093 (Rfree = 0.000) for 888 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 29: After refmac, R = 0.3198 (Rfree = 0.000) for 882 atoms. Found 6 (6 requested) and removed 6 (3 requested) atoms. Cycle 30: After refmac, R = 0.3195 (Rfree = 0.000) for 879 atoms. Found 6 (6 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.41 3.28 Search for helices and strands: 0 residues in 0 chains, 945 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 6 peptides. Score 0.236 Round 2: 64 peptides, 13 chains. Longest chain 8 peptides. Score 0.300 Round 3: 61 peptides, 11 chains. Longest chain 14 peptides. Score 0.356 Round 4: 64 peptides, 12 chains. Longest chain 12 peptides. Score 0.343 Round 5: 65 peptides, 12 chains. Longest chain 11 peptides. Score 0.353 Taking the results from Round 3 Chains 11, Residues 50, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2543 reflections ( 99.45 % complete ) and 1988 restraints for refining 932 atoms. 1799 conditional restraints added. Observations/parameters ratio is 0.68 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3753 (Rfree = 0.000) for 932 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 32: After refmac, R = 0.3779 (Rfree = 0.000) for 924 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 33: After refmac, R = 0.3499 (Rfree = 0.000) for 914 atoms. Found 6 (6 requested) and removed 10 (3 requested) atoms. Cycle 34: After refmac, R = 0.3373 (Rfree = 0.000) for 908 atoms. Found 6 (6 requested) and removed 5 (3 requested) atoms. Cycle 35: After refmac, R = 0.3348 (Rfree = 0.000) for 906 atoms. Found 6 (6 requested) and removed 8 (3 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.46 3.32 Search for helices and strands: 0 residues in 0 chains, 965 seeds are put forward Round 1: 44 peptides, 9 chains. Longest chain 7 peptides. Score 0.265 Round 2: 64 peptides, 11 chains. Longest chain 9 peptides. Score 0.386 Round 3: 69 peptides, 12 chains. Longest chain 10 peptides. Score 0.393 Round 4: 64 peptides, 10 chains. Longest chain 10 peptides. Score 0.428 Round 5: 58 peptides, 10 chains. Longest chain 11 peptides. Score 0.370 Taking the results from Round 4 Chains 10, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2543 reflections ( 99.45 % complete ) and 1899 restraints for refining 923 atoms. 1693 conditional restraints added. Observations/parameters ratio is 0.69 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3567 (Rfree = 0.000) for 923 atoms. Found 6 (6 requested) and removed 7 (3 requested) atoms. Cycle 37: After refmac, R = 0.3868 (Rfree = 0.000) for 913 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 38: After refmac, R = 0.3652 (Rfree = 0.000) for 893 atoms. Found 6 (6 requested) and removed 17 (3 requested) atoms. Cycle 39: After refmac, R = 0.3186 (Rfree = 0.000) for 875 atoms. Found 1 (6 requested) and removed 106 (3 requested) atoms. Cycle 40: After refmac, R = 0.3936 (Rfree = 0.000) for 763 atoms. Found 5 (5 requested) and removed 10 (2 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.48 3.34 Search for helices and strands: 0 residues in 0 chains, 796 seeds are put forward Round 1: 49 peptides, 11 chains. Longest chain 7 peptides. Score 0.226 Round 2: 50 peptides, 11 chains. Longest chain 6 peptides. Score 0.238 Round 3: 59 peptides, 11 chains. Longest chain 10 peptides. Score 0.336 Round 4: 60 peptides, 12 chains. Longest chain 8 peptides. Score 0.302 Round 5: 51 peptides, 10 chains. Longest chain 7 peptides. Score 0.296 Taking the results from Round 3 Chains 11, Residues 48, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2543 reflections ( 99.45 % complete ) and 1554 restraints for refining 793 atoms. 1373 conditional restraints added. Observations/parameters ratio is 0.80 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3823 (Rfree = 0.000) for 793 atoms. Found 5 (5 requested) and removed 7 (2 requested) atoms. Cycle 42: After refmac, R = 0.3687 (Rfree = 0.000) for 787 atoms. Found 5 (5 requested) and removed 5 (2 requested) atoms. Cycle 43: After refmac, R = 0.3876 (Rfree = 0.000) for 783 atoms. Found 5 (5 requested) and removed 11 (2 requested) atoms. Cycle 44: After refmac, R = 0.3507 (Rfree = 0.000) for 772 atoms. Found 5 (5 requested) and removed 4 (2 requested) atoms. Cycle 45: After refmac, R = 0.3043 (Rfree = 0.000) for 770 atoms. Found 5 (5 requested) and removed 2 (2 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.48 3.34 Search for helices and strands: 0 residues in 0 chains, 799 seeds are put forward Round 1: 54 peptides, 12 chains. Longest chain 6 peptides. Score 0.236 Round 2: 54 peptides, 11 chains. Longest chain 9 peptides. Score 0.283 Round 3: 48 peptides, 10 chains. Longest chain 6 peptides. Score 0.263 Round 4: 54 peptides, 10 chains. Longest chain 7 peptides. Score 0.328 Round 5: 50 peptides, 10 chains. Longest chain 8 peptides. Score 0.285 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 44, 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 2pv4-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2543 reflections ( 99.45 % complete ) and 1732 restraints for refining 827 atoms. 1566 conditional restraints added. Observations/parameters ratio is 0.77 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3439 (Rfree = 0.000) for 827 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3699 (Rfree = 0.000) for 816 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.3470 (Rfree = 0.000) for 809 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3675 (Rfree = 0.000) for 802 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. TimeTaking 23.03