null Tue 25 Dec 19:27:55 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 2od5-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2od5-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2od5-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-4.0-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/2od5-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-4.0-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 ============================================================ Tue 25 Dec 19:28:05 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/2od5-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2od5-4.0-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 99 and 0 Target number of residues in the AU: 99 Target solvent content: 0.6645 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: 2od5-4.0-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: 180 Cell parameters: 64.428 64.428 133.292 90.000 90.000 120.000 Input sequence file: 2od5-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 928 target number of atoms Had to go as low as 0.90 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 4.001 Wilson plot Bfac: 87.34 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 1609 reflections ( 99.51 % complete ) and 0 restraints for refining 1023 atoms. Observations/parameters ratio is 0.39 ------------------------------------------------------ Starting model: R = 0.3894 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.4169 (Rfree = 0.000) for 1023 atoms. Found 4 (4 requested) and removed 12 (2 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.84 3.31 Search for helices and strands: 0 residues in 0 chains, 1040 seeds are put forward Round 1: 48 peptides, 8 chains. Longest chain 11 peptides. Score 0.363 Round 2: 57 peptides, 7 chains. Longest chain 13 peptides. Score 0.499 Round 3: 56 peptides, 6 chains. Longest chain 17 peptides. Score 0.532 Round 4: 58 peptides, 4 chains. Longest chain 26 peptides. Score 0.628 Round 5: 65 peptides, 9 chains. Longest chain 13 peptides. Score 0.488 Taking the results from Round 4 Chains 4, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1609 reflections ( 99.51 % complete ) and 1794 restraints for refining 779 atoms. 1582 conditional restraints added. Observations/parameters ratio is 0.52 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3512 (Rfree = 0.000) for 779 atoms. Found 3 (3 requested) and removed 6 (1 requested) atoms. Cycle 2: After refmac, R = 0.3535 (Rfree = 0.000) for 760 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 3: After refmac, R = 0.2963 (Rfree = 0.000) for 749 atoms. Found 0 (3 requested) and removed 5 (1 requested) atoms. Cycle 4: After refmac, R = 0.2949 (Rfree = 0.000) for 741 atoms. Found 2 (3 requested) and removed 5 (1 requested) atoms. Cycle 5: After refmac, R = 0.2837 (Rfree = 0.000) for 733 atoms. Found 3 (3 requested) and removed 13 (1 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.16 Search for helices and strands: 0 residues in 0 chains, 757 seeds are put forward Round 1: 55 peptides, 8 chains. Longest chain 12 peptides. Score 0.436 Round 2: 62 peptides, 6 chains. Longest chain 19 peptides. Score 0.582 Round 3: 51 peptides, 6 chains. Longest chain 18 peptides. Score 0.486 Round 4: 59 peptides, 7 chains. Longest chain 21 peptides. Score 0.517 Round 5: 54 peptides, 6 chains. Longest chain 11 peptides. Score 0.514 Taking the results from Round 2 Chains 6, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1609 reflections ( 99.51 % complete ) and 1609 restraints for refining 736 atoms. 1391 conditional restraints added. Observations/parameters ratio is 0.55 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3438 (Rfree = 0.000) for 736 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. Cycle 7: After refmac, R = 0.3198 (Rfree = 0.000) for 726 atoms. Found 3 (3 requested) and removed 8 (1 requested) atoms. Cycle 8: After refmac, R = 0.3618 (Rfree = 0.000) for 713 atoms. Found 3 (3 requested) and removed 17 (1 requested) atoms. Cycle 9: After refmac, R = 0.3136 (Rfree = 0.000) for 697 atoms. Found 1 (3 requested) and removed 1 (1 requested) atoms. Cycle 10: After refmac, R = 0.2831 (Rfree = 0.000) for 694 atoms. Found 1 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.69 3.18 Search for helices and strands: 0 residues in 0 chains, 739 seeds are put forward Round 1: 61 peptides, 7 chains. Longest chain 18 peptides. Score 0.534 Round 2: 61 peptides, 5 chains. Longest chain 19 peptides. Score 0.613 Round 3: 67 peptides, 7 chains. Longest chain 20 peptides. Score 0.584 Round 4: 67 peptides, 9 chains. Longest chain 18 peptides. Score 0.506 Round 5: 68 peptides, 9 chains. Longest chain 17 peptides. Score 0.515 Taking the results from Round 2 Chains 5, Residues 56, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1609 reflections ( 99.51 % complete ) and 1622 restraints for refining 745 atoms. 1403 conditional restraints added. Observations/parameters ratio is 0.54 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3267 (Rfree = 0.000) for 745 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 12: After refmac, R = 0.3091 (Rfree = 0.000) for 731 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 13: After refmac, R = 0.3034 (Rfree = 0.000) for 724 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. Cycle 14: After refmac, R = 0.3077 (Rfree = 0.000) for 723 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 15: After refmac, R = 0.2780 (Rfree = 0.000) for 716 atoms. Found 3 (3 requested) and removed 1 (1 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.82 3.29 Search for helices and strands: 0 residues in 0 chains, 741 seeds are put forward Round 1: 54 peptides, 7 chains. Longest chain 15 peptides. Score 0.471 Round 2: 55 peptides, 7 chains. Longest chain 14 peptides. Score 0.480 Round 3: 59 peptides, 7 chains. Longest chain 18 peptides. Score 0.517 Round 4: 66 peptides, 8 chains. Longest chain 14 peptides. Score 0.537 Round 5: 65 peptides, 6 chains. Longest chain 21 peptides. Score 0.606 Taking the results from Round 5 Chains 6, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1609 reflections ( 99.51 % complete ) and 1650 restraints for refining 762 atoms. 1420 conditional restraints added. Observations/parameters ratio is 0.53 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3247 (Rfree = 0.000) for 762 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 17: After refmac, R = 0.3134 (Rfree = 0.000) for 751 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 18: After refmac, R = 0.3232 (Rfree = 0.000) for 745 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 19: After refmac, R = 0.3217 (Rfree = 0.000) for 742 atoms. Found 3 (3 requested) and removed 10 (1 requested) atoms. Cycle 20: After refmac, R = 0.2920 (Rfree = 0.000) for 730 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.83 3.30 Search for helices and strands: 0 residues in 0 chains, 768 seeds are put forward Round 1: 62 peptides, 9 chains. Longest chain 21 peptides. Score 0.460 Round 2: 58 peptides, 9 chains. Longest chain 11 peptides. Score 0.421 Round 3: 62 peptides, 8 chains. Longest chain 21 peptides. Score 0.502 Round 4: 61 peptides, 6 chains. Longest chain 21 peptides. Score 0.574 Round 5: 66 peptides, 7 chains. Longest chain 18 peptides. Score 0.576 Taking the results from Round 5 Chains 7, Residues 59, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1609 reflections ( 99.51 % complete ) and 1751 restraints for refining 789 atoms. 1522 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3167 (Rfree = 0.000) for 789 atoms. Found 3 (3 requested) and removed 9 (1 requested) atoms. Cycle 22: After refmac, R = 0.3317 (Rfree = 0.000) for 777 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 23: After refmac, R = 0.3703 (Rfree = 0.000) for 768 atoms. Found 3 (3 requested) and removed 10 (1 requested) atoms. Cycle 24: After refmac, R = 0.3451 (Rfree = 0.000) for 751 atoms. Found 3 (3 requested) and removed 6 (1 requested) atoms. Cycle 25: After refmac, R = 0.3132 (Rfree = 0.000) for 741 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.83 3.30 Search for helices and strands: 0 residues in 0 chains, 788 seeds are put forward Round 1: 50 peptides, 7 chains. Longest chain 12 peptides. Score 0.431 Round 2: 54 peptides, 8 chains. Longest chain 11 peptides. Score 0.426 Round 3: 61 peptides, 7 chains. Longest chain 16 peptides. Score 0.534 Round 4: 62 peptides, 8 chains. Longest chain 15 peptides. Score 0.502 Round 5: 59 peptides, 7 chains. Longest chain 12 peptides. Score 0.517 Taking the results from Round 3 Chains 7, Residues 54, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1609 reflections ( 99.51 % complete ) and 1778 restraints for refining 788 atoms. 1569 conditional restraints added. Observations/parameters ratio is 0.51 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3364 (Rfree = 0.000) for 788 atoms. Found 3 (3 requested) and removed 8 (1 requested) atoms. Cycle 27: After refmac, R = 0.3021 (Rfree = 0.000) for 774 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 28: After refmac, R = 0.3229 (Rfree = 0.000) for 768 atoms. Found 3 (3 requested) and removed 5 (1 requested) atoms. Cycle 29: After refmac, R = 0.3321 (Rfree = 0.000) for 762 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 30: After refmac, R = 0.3085 (Rfree = 0.000) for 759 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.84 3.31 Search for helices and strands: 0 residues in 0 chains, 782 seeds are put forward Round 1: 59 peptides, 10 chains. Longest chain 11 peptides. Score 0.387 Round 2: 62 peptides, 8 chains. Longest chain 17 peptides. Score 0.502 Round 3: 61 peptides, 8 chains. Longest chain 19 peptides. Score 0.493 Round 4: 55 peptides, 9 chains. Longest chain 11 peptides. Score 0.391 Round 5: 60 peptides, 7 chains. Longest chain 19 peptides. Score 0.525 Taking the results from Round 5 Chains 7, Residues 53, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1609 reflections ( 99.51 % complete ) and 1868 restraints for refining 814 atoms. 1663 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3528 (Rfree = 0.000) for 814 atoms. Found 3 (3 requested) and removed 7 (1 requested) atoms. Cycle 32: After refmac, R = 0.3470 (Rfree = 0.000) for 803 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 33: After refmac, R = 0.2927 (Rfree = 0.000) for 799 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 34: After refmac, R = 0.2983 (Rfree = 0.000) for 794 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 35: After refmac, R = 0.3311 (Rfree = 0.000) for 791 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.79 3.27 Search for helices and strands: 0 residues in 0 chains, 824 seeds are put forward Round 1: 51 peptides, 9 chains. Longest chain 10 peptides. Score 0.348 Round 2: 57 peptides, 10 chains. Longest chain 10 peptides. Score 0.366 Round 3: 61 peptides, 8 chains. Longest chain 14 peptides. Score 0.493 Round 4: 65 peptides, 9 chains. Longest chain 16 peptides. Score 0.488 Round 5: 67 peptides, 9 chains. Longest chain 18 peptides. Score 0.506 Taking the results from Round 5 Chains 9, Residues 58, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1609 reflections ( 99.51 % complete ) and 1921 restraints for refining 837 atoms. 1698 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3333 (Rfree = 0.000) for 837 atoms. Found 3 (3 requested) and removed 8 (1 requested) atoms. Cycle 37: After refmac, R = 0.3138 (Rfree = 0.000) for 827 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 38: After refmac, R = 0.3525 (Rfree = 0.000) for 821 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. Cycle 39: After refmac, R = 0.3252 (Rfree = 0.000) for 816 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 40: After refmac, R = 0.3081 (Rfree = 0.000) for 811 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.78 3.26 Search for helices and strands: 0 residues in 0 chains, 846 seeds are put forward Round 1: 44 peptides, 8 chains. Longest chain 14 peptides. Score 0.319 Round 2: 55 peptides, 9 chains. Longest chain 16 peptides. Score 0.391 Round 3: 51 peptides, 7 chains. Longest chain 13 peptides. Score 0.441 Round 4: 52 peptides, 7 chains. Longest chain 21 peptides. Score 0.451 Round 5: 48 peptides, 7 chains. Longest chain 13 peptides. Score 0.411 Taking the results from Round 4 Chains 7, Residues 45, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 1609 reflections ( 99.51 % complete ) and 2048 restraints for refining 838 atoms. 1875 conditional restraints added. Observations/parameters ratio is 0.48 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3471 (Rfree = 0.000) for 838 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 42: After refmac, R = 0.3229 (Rfree = 0.000) for 832 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 43: After refmac, R = 0.3349 (Rfree = 0.000) for 828 atoms. Found 3 (3 requested) and removed 3 (1 requested) atoms. Cycle 44: After refmac, R = 0.3302 (Rfree = 0.000) for 824 atoms. Found 3 (3 requested) and removed 4 (1 requested) atoms. Cycle 45: After refmac, R = 0.3017 (Rfree = 0.000) for 819 atoms. Found 3 (3 requested) and removed 2 (1 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.94 3.39 Search for helices and strands: 0 residues in 0 chains, 845 seeds are put forward Round 1: 44 peptides, 6 chains. Longest chain 16 peptides. Score 0.417 Round 2: 55 peptides, 9 chains. Longest chain 12 peptides. Score 0.391 Round 3: 50 peptides, 6 chains. Longest chain 15 peptides. Score 0.477 Round 4: 53 peptides, 6 chains. Longest chain 26 peptides. Score 0.505 Round 5: 50 peptides, 8 chains. Longest chain 17 peptides. Score 0.385 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 47, 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 2od5-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 1609 reflections ( 99.51 % complete ) and 1879 restraints for refining 822 atoms. 1697 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3744 (Rfree = 0.000) for 822 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 47: After refmac, R = 0.3366 (Rfree = 0.000) for 811 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 48: After refmac, R = 0.3665 (Rfree = 0.000) for 799 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Cycle 49: After refmac, R = 0.3711 (Rfree = 0.000) for 793 atoms. Found 0 (3 requested) and removed 1 (1 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 19:57:59 GMT 2018 Job finished. TimeTaking 30.07 Used memory is bytes: 13416784