null Sun 23 Dec 22:22:53 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 2gno-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2gno-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2gno-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-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/2gno-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-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 22:23:03 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/2gno-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2gno-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 185 and 0 Target number of residues in the AU: 185 Target solvent content: 0.6936 Checking the provided sequence file Detected sequence length: 305 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 305 Adjusted target solvent content: 0.49 Input MTZ file: 2gno-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: 79 Cell parameters: 135.560 135.560 35.560 90.000 90.000 90.000 Input sequence file: 2gno-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2440 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: 95.855 4.000 Wilson plot Bfac: 113.79 2860 reflections ( 98.59 % complete ) and 0 restraints for refining 2686 atoms. Observations/parameters ratio is 0.27 ------------------------------------------------------ Starting model: R = 0.3573 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3805 (Rfree = 0.000) for 2686 atoms. Found 12 (12 requested) and removed 43 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 4.00 4.05 Search for helices and strands: 0 residues in 0 chains, 2703 seeds are put forward Round 1: 45 peptides, 10 chains. Longest chain 6 peptides. Score 0.207 Round 2: 69 peptides, 15 chains. Longest chain 6 peptides. Score 0.228 Round 3: 80 peptides, 17 chains. Longest chain 6 peptides. Score 0.244 Round 4: 97 peptides, 20 chains. Longest chain 7 peptides. Score 0.270 Round 5: 95 peptides, 17 chains. Longest chain 7 peptides. Score 0.331 Taking the results from Round 5 Chains 17, Residues 78, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2860 reflections ( 98.59 % complete ) and 4809 restraints for refining 2012 atoms. 4514 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3375 (Rfree = 0.000) for 2012 atoms. Found 3 (9 requested) and removed 18 (4 requested) atoms. Cycle 2: After refmac, R = 0.3086 (Rfree = 0.000) for 1956 atoms. Found 9 (9 requested) and removed 17 (4 requested) atoms. Cycle 3: After refmac, R = 0.3215 (Rfree = 0.000) for 1923 atoms. Found 4 (9 requested) and removed 16 (4 requested) atoms. Cycle 4: After refmac, R = 0.2941 (Rfree = 0.000) for 1897 atoms. Found 6 (9 requested) and removed 12 (4 requested) atoms. Cycle 5: After refmac, R = 0.3041 (Rfree = 0.000) for 1876 atoms. Found 4 (8 requested) and removed 18 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.98 4.03 Search for helices and strands: 0 residues in 0 chains, 1943 seeds are put forward Round 1: 100 peptides, 21 chains. Longest chain 8 peptides. Score 0.263 Round 2: 111 peptides, 20 chains. Longest chain 10 peptides. Score 0.347 Round 3: 107 peptides, 20 chains. Longest chain 11 peptides. Score 0.326 Round 4: 110 peptides, 17 chains. Longest chain 17 peptides. Score 0.410 Round 5: 113 peptides, 16 chains. Longest chain 18 peptides. Score 0.447 Taking the results from Round 5 Chains 17, Residues 97, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 2860 reflections ( 98.59 % complete ) and 4184 restraints for refining 1938 atoms. 3767 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2995 (Rfree = 0.000) for 1938 atoms. Found 6 (9 requested) and removed 22 (4 requested) atoms. Cycle 7: After refmac, R = 0.2970 (Rfree = 0.000) for 1887 atoms. Found 9 (9 requested) and removed 20 (4 requested) atoms. Cycle 8: After refmac, R = 0.2526 (Rfree = 0.000) for 1850 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 9: After refmac, R = 0.2855 (Rfree = 0.000) for 1823 atoms. Found 8 (8 requested) and removed 47 (4 requested) atoms. Cycle 10: After refmac, R = 0.3063 (Rfree = 0.000) for 1764 atoms. Found 8 (8 requested) and removed 21 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 4.04 4.09 Search for helices and strands: 0 residues in 0 chains, 1814 seeds are put forward Round 1: 87 peptides, 18 chains. Longest chain 10 peptides. Score 0.261 Round 2: 96 peptides, 16 chains. Longest chain 10 peptides. Score 0.361 Round 3: 106 peptides, 17 chains. Longest chain 11 peptides. Score 0.390 Round 4: 107 peptides, 16 chains. Longest chain 11 peptides. Score 0.417 Round 5: 109 peptides, 17 chains. Longest chain 12 peptides. Score 0.405 Taking the results from Round 4 Chains 16, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2860 reflections ( 98.59 % complete ) and 3788 restraints for refining 1771 atoms. 3440 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3062 (Rfree = 0.000) for 1771 atoms. Found 6 (8 requested) and removed 11 (4 requested) atoms. Cycle 12: After refmac, R = 0.3073 (Rfree = 0.000) for 1745 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 13: After refmac, R = 0.3145 (Rfree = 0.000) for 1720 atoms. Found 8 (8 requested) and removed 9 (4 requested) atoms. Cycle 14: After refmac, R = 0.2944 (Rfree = 0.000) for 1693 atoms. Found 7 (8 requested) and removed 9 (4 requested) atoms. Cycle 15: After refmac, R = 0.2374 (Rfree = 0.000) for 1680 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.94 3.99 Search for helices and strands: 0 residues in 0 chains, 1748 seeds are put forward Round 1: 88 peptides, 17 chains. Longest chain 9 peptides. Score 0.292 Round 2: 108 peptides, 21 chains. Longest chain 9 peptides. Score 0.308 Round 3: 110 peptides, 19 chains. Longest chain 11 peptides. Score 0.365 Round 4: 115 peptides, 20 chains. Longest chain 10 peptides. Score 0.368 Round 5: 117 peptides, 19 chains. Longest chain 12 peptides. Score 0.401 Taking the results from Round 5 Chains 19, Residues 98, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2860 reflections ( 98.59 % complete ) and 3935 restraints for refining 1793 atoms. 3562 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2893 (Rfree = 0.000) for 1793 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 17: After refmac, R = 0.3073 (Rfree = 0.000) for 1757 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 18: After refmac, R = 0.2623 (Rfree = 0.000) for 1732 atoms. Found 7 (8 requested) and removed 6 (4 requested) atoms. Cycle 19: After refmac, R = 0.2794 (Rfree = 0.000) for 1716 atoms. Found 8 (8 requested) and removed 7 (4 requested) atoms. Cycle 20: After refmac, R = 0.3026 (Rfree = 0.000) for 1702 atoms. Found 4 (8 requested) and removed 16 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.93 3.98 Search for helices and strands: 0 residues in 0 chains, 1764 seeds are put forward Round 1: 74 peptides, 15 chains. Longest chain 7 peptides. Score 0.259 Round 2: 98 peptides, 18 chains. Longest chain 9 peptides. Score 0.324 Round 3: 106 peptides, 20 chains. Longest chain 9 peptides. Score 0.320 Round 4: 95 peptides, 16 chains. Longest chain 12 peptides. Score 0.355 Round 5: 102 peptides, 17 chains. Longest chain 10 peptides. Score 0.369 Taking the results from Round 5 Chains 17, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2860 reflections ( 98.59 % complete ) and 3949 restraints for refining 1767 atoms. 3626 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.3058 (Rfree = 0.000) for 1767 atoms. Found 8 (8 requested) and removed 25 (4 requested) atoms. Cycle 22: After refmac, R = 0.2901 (Rfree = 0.000) for 1737 atoms. Found 8 (8 requested) and removed 12 (4 requested) atoms. Cycle 23: After refmac, R = 0.2710 (Rfree = 0.000) for 1722 atoms. Found 7 (8 requested) and removed 10 (4 requested) atoms. Cycle 24: After refmac, R = 0.2964 (Rfree = 0.000) for 1705 atoms. Found 8 (8 requested) and removed 14 (4 requested) atoms. Cycle 25: After refmac, R = 0.2909 (Rfree = 0.000) for 1686 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.97 4.02 Search for helices and strands: 0 residues in 0 chains, 1754 seeds are put forward Round 1: 87 peptides, 20 chains. Longest chain 6 peptides. Score 0.211 Round 2: 97 peptides, 17 chains. Longest chain 10 peptides. Score 0.342 Round 3: 105 peptides, 18 chains. Longest chain 11 peptides. Score 0.362 Round 4: 102 peptides, 18 chains. Longest chain 10 peptides. Score 0.346 Round 5: 103 peptides, 19 chains. Longest chain 9 peptides. Score 0.328 Taking the results from Round 3 Chains 18, Residues 87, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2860 reflections ( 98.59 % complete ) and 3601 restraints for refining 1713 atoms. 3271 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 26: After refmac, R = 0.3146 (Rfree = 0.000) for 1713 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 27: After refmac, R = 0.2895 (Rfree = 0.000) for 1697 atoms. Found 8 (8 requested) and removed 13 (4 requested) atoms. Cycle 28: After refmac, R = 0.2604 (Rfree = 0.000) for 1678 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 29: After refmac, R = 0.2902 (Rfree = 0.000) for 1666 atoms. Found 7 (7 requested) and removed 10 (3 requested) atoms. Cycle 30: After refmac, R = 0.2617 (Rfree = 0.000) for 1656 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 4.04 4.09 Search for helices and strands: 0 residues in 0 chains, 1704 seeds are put forward Round 1: 93 peptides, 21 chains. Longest chain 6 peptides. Score 0.222 Round 2: 97 peptides, 17 chains. Longest chain 11 peptides. Score 0.342 Round 3: 100 peptides, 19 chains. Longest chain 7 peptides. Score 0.311 Round 4: 107 peptides, 19 chains. Longest chain 12 peptides. Score 0.349 Round 5: 104 peptides, 16 chains. Longest chain 11 peptides. Score 0.402 Taking the results from Round 5 Chains 16, Residues 88, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2860 reflections ( 98.59 % complete ) and 3875 restraints for refining 1761 atoms. 3539 conditional restraints added. Observations/parameters ratio is 0.41 ------------------------------------------------------ Cycle 31: After refmac, R = 0.3043 (Rfree = 0.000) for 1761 atoms. Found 8 (8 requested) and removed 18 (4 requested) atoms. Cycle 32: After refmac, R = 0.3031 (Rfree = 0.000) for 1723 atoms. Found 8 (8 requested) and removed 10 (4 requested) atoms. Cycle 33: After refmac, R = 0.2737 (Rfree = 0.000) for 1703 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 34: After refmac, R = 0.2680 (Rfree = 0.000) for 1689 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 35: After refmac, R = 0.2293 (Rfree = 0.000) for 1673 atoms. Found 3 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.94 3.99 Search for helices and strands: 0 residues in 0 chains, 1717 seeds are put forward Round 1: 71 peptides, 15 chains. Longest chain 8 peptides. Score 0.241 Round 2: 87 peptides, 18 chains. Longest chain 7 peptides. Score 0.261 Round 3: 91 peptides, 18 chains. Longest chain 6 peptides. Score 0.284 Round 4: 79 peptides, 15 chains. Longest chain 10 peptides. Score 0.290 Round 5: 81 peptides, 16 chains. Longest chain 7 peptides. Score 0.276 Taking the results from Round 4 Chains 15, Residues 64, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2860 reflections ( 98.59 % complete ) and 3693 restraints for refining 1645 atoms. 3452 conditional restraints added. Observations/parameters ratio is 0.43 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3123 (Rfree = 0.000) for 1645 atoms. Found 7 (7 requested) and removed 12 (3 requested) atoms. Cycle 37: After refmac, R = 0.2856 (Rfree = 0.000) for 1625 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 38: After refmac, R = 0.3080 (Rfree = 0.000) for 1615 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 39: After refmac, R = 0.2942 (Rfree = 0.000) for 1608 atoms. Found 7 (7 requested) and removed 4 (3 requested) atoms. Cycle 40: After refmac, R = 0.2793 (Rfree = 0.000) for 1601 atoms. Found 7 (7 requested) and removed 3 (3 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 4.01 4.06 Search for helices and strands: 0 residues in 0 chains, 1647 seeds are put forward Round 1: 68 peptides, 15 chains. Longest chain 6 peptides. Score 0.221 Round 2: 72 peptides, 12 chains. Longest chain 10 peptides. Score 0.327 Round 3: 73 peptides, 12 chains. Longest chain 12 peptides. Score 0.332 Round 4: 71 peptides, 14 chains. Longest chain 10 peptides. Score 0.267 Round 5: 66 peptides, 12 chains. Longest chain 10 peptides. Score 0.291 Taking the results from Round 3 Chains 12, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 2860 reflections ( 98.59 % complete ) and 3360 restraints for refining 1581 atoms. 3128 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3007 (Rfree = 0.000) for 1581 atoms. Found 7 (7 requested) and removed 8 (3 requested) atoms. Cycle 42: After refmac, R = 0.2780 (Rfree = 0.000) for 1562 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. Cycle 43: After refmac, R = 0.2445 (Rfree = 0.000) for 1554 atoms. Found 4 (7 requested) and removed 5 (3 requested) atoms. Cycle 44: After refmac, R = 0.2943 (Rfree = 0.000) for 1543 atoms. Found 7 (7 requested) and removed 9 (3 requested) atoms. Cycle 45: After refmac, R = 0.2970 (Rfree = 0.000) for 1535 atoms. Found 7 (7 requested) and removed 6 (3 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.95 4.00 Search for helices and strands: 0 residues in 0 chains, 1571 seeds are put forward Round 1: 57 peptides, 12 chains. Longest chain 9 peptides. Score 0.232 Round 2: 51 peptides, 10 chains. Longest chain 10 peptides. Score 0.251 Round 3: 61 peptides, 11 chains. Longest chain 12 peptides. Score 0.287 Round 4: 62 peptides, 10 chains. Longest chain 14 peptides. Score 0.322 Round 5: 54 peptides, 10 chains. Longest chain 10 peptides. Score 0.271 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 10, Residues 52, 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 2gno-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 2860 reflections ( 98.59 % complete ) and 2970 restraints for refining 1454 atoms. 2772 conditional restraints added. Observations/parameters ratio is 0.49 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3136 (Rfree = 0.000) for 1454 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 47: After refmac, R = 0.3374 (Rfree = 0.000) for 1441 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 48: After refmac, R = 0.2969 (Rfree = 0.000) for 1430 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Cycle 49: After refmac, R = 0.3249 (Rfree = 0.000) for 1422 atoms. Found 0 (6 requested) and removed 3 (3 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 22:55:56 GMT 2018 Job finished. TimeTaking 33.05 Used memory is bytes: 4295152