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 2fur-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2fur-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2fur-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-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/2fur-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-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 22:23:07 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/2fur-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2fur-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 245 and 0 Target number of residues in the AU: 245 Target solvent content: 0.6741 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 418 Adjusted target solvent content: 0.44 Input MTZ file: 2fur-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: 19 Cell parameters: 61.040 66.690 99.940 90.000 90.000 90.000 Input sequence file: 2fur-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3344 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 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 55.473 4.000 Wilson plot Bfac: 95.59 3709 reflections ( 99.52 % complete ) and 0 restraints for refining 3710 atoms. Observations/parameters ratio is 0.25 ------------------------------------------------------ Starting model: R = 0.3313 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3397 (Rfree = 0.000) for 3710 atoms. Found 15 (17 requested) and removed 75 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.81 4.13 Search for helices and strands: 0 residues in 0 chains, 3737 seeds are put forward NCS extension: 0 residues added, 3737 seeds are put forward Round 1: 146 peptides, 28 chains. Longest chain 10 peptides. Score 0.324 Round 2: 199 peptides, 29 chains. Longest chain 18 peptides. Score 0.511 Round 3: 199 peptides, 27 chains. Longest chain 19 peptides. Score 0.541 Round 4: 218 peptides, 28 chains. Longest chain 15 peptides. Score 0.587 Round 5: 207 peptides, 25 chains. Longest chain 27 peptides. Score 0.594 Taking the results from Round 5 Chains 28, Residues 182, Estimated correctness of the model 0.0 % 2 chains (21 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6960 restraints for refining 3020 atoms. 6194 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2398 (Rfree = 0.000) for 3020 atoms. Found 13 (14 requested) and removed 22 (7 requested) atoms. Cycle 2: After refmac, R = 0.2299 (Rfree = 0.000) for 2949 atoms. Found 8 (14 requested) and removed 19 (7 requested) atoms. Cycle 3: After refmac, R = 0.1836 (Rfree = 0.000) for 2897 atoms. Found 2 (13 requested) and removed 8 (6 requested) atoms. Cycle 4: After refmac, R = 0.1697 (Rfree = 0.000) for 2868 atoms. Found 2 (13 requested) and removed 10 (6 requested) atoms. Cycle 5: After refmac, R = 0.1640 (Rfree = 0.000) for 2838 atoms. Found 0 (13 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.83 4.15 Search for helices and strands: 0 residues in 0 chains, 2929 seeds are put forward NCS extension: 34 residues added (1 deleted due to clashes), 2963 seeds are put forward Round 1: 164 peptides, 32 chains. Longest chain 11 peptides. Score 0.329 Round 2: 200 peptides, 30 chains. Longest chain 16 peptides. Score 0.500 Round 3: 185 peptides, 29 chains. Longest chain 13 peptides. Score 0.462 Round 4: 192 peptides, 27 chains. Longest chain 17 peptides. Score 0.518 Round 5: 204 peptides, 30 chains. Longest chain 17 peptides. Score 0.513 Taking the results from Round 4 Chains 29, Residues 165, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6749 restraints for refining 2912 atoms. 6082 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2372 (Rfree = 0.000) for 2912 atoms. Found 1 (13 requested) and removed 34 (6 requested) atoms. Cycle 7: After refmac, R = 0.2238 (Rfree = 0.000) for 2854 atoms. Found 6 (13 requested) and removed 23 (6 requested) atoms. Cycle 8: After refmac, R = 0.2117 (Rfree = 0.000) for 2822 atoms. Found 9 (13 requested) and removed 23 (6 requested) atoms. Cycle 9: After refmac, R = 0.2095 (Rfree = 0.000) for 2790 atoms. Found 8 (13 requested) and removed 30 (6 requested) atoms. Cycle 10: After refmac, R = 0.2009 (Rfree = 0.000) for 2760 atoms. Found 5 (13 requested) and removed 20 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.72 4.03 Search for helices and strands: 0 residues in 0 chains, 2883 seeds are put forward NCS extension: 18 residues added (2 deleted due to clashes), 2901 seeds are put forward Round 1: 172 peptides, 36 chains. Longest chain 8 peptides. Score 0.292 Round 2: 192 peptides, 32 chains. Longest chain 12 peptides. Score 0.440 Round 3: 180 peptides, 31 chains. Longest chain 14 peptides. Score 0.410 Round 4: 182 peptides, 26 chains. Longest chain 18 peptides. Score 0.499 Round 5: 191 peptides, 31 chains. Longest chain 15 peptides. Score 0.452 Taking the results from Round 4 Chains 26, Residues 156, Estimated correctness of the model 0.0 % 2 chains (20 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6476 restraints for refining 2930 atoms. 5806 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2204 (Rfree = 0.000) for 2930 atoms. Found 12 (13 requested) and removed 32 (6 requested) atoms. Cycle 12: After refmac, R = 0.2144 (Rfree = 0.000) for 2887 atoms. Found 13 (13 requested) and removed 21 (6 requested) atoms. Cycle 13: After refmac, R = 0.2067 (Rfree = 0.000) for 2863 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 14: After refmac, R = 0.1397 (Rfree = 0.000) for 2845 atoms. Found 3 (13 requested) and removed 11 (6 requested) atoms. Cycle 15: After refmac, R = 0.1292 (Rfree = 0.000) for 2827 atoms. Found 0 (13 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.84 4.16 Search for helices and strands: 0 residues in 0 chains, 2900 seeds are put forward NCS extension: 0 residues added, 2900 seeds are put forward Round 1: 165 peptides, 34 chains. Longest chain 9 peptides. Score 0.297 Round 2: 184 peptides, 33 chains. Longest chain 16 peptides. Score 0.393 Round 3: 188 peptides, 32 chains. Longest chain 12 peptides. Score 0.425 Round 4: 200 peptides, 28 chains. Longest chain 18 peptides. Score 0.530 Round 5: 199 peptides, 32 chains. Longest chain 16 peptides. Score 0.465 Taking the results from Round 4 Chains 28, Residues 172, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6776 restraints for refining 2951 atoms. 6116 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2030 (Rfree = 0.000) for 2951 atoms. Found 11 (14 requested) and removed 26 (7 requested) atoms. Cycle 17: After refmac, R = 0.2184 (Rfree = 0.000) for 2919 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 18: After refmac, R = 0.2144 (Rfree = 0.000) for 2903 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 19: After refmac, R = 0.2064 (Rfree = 0.000) for 2897 atoms. Found 13 (13 requested) and removed 18 (6 requested) atoms. Cycle 20: After refmac, R = 0.2296 (Rfree = 0.000) for 2883 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.84 4.16 Search for helices and strands: 0 residues in 0 chains, 3004 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 3024 seeds are put forward Round 1: 144 peptides, 28 chains. Longest chain 9 peptides. Score 0.315 Round 2: 173 peptides, 26 chains. Longest chain 13 peptides. Score 0.466 Round 3: 179 peptides, 25 chains. Longest chain 16 peptides. Score 0.504 Round 4: 168 peptides, 26 chains. Longest chain 13 peptides. Score 0.448 Round 5: 169 peptides, 25 chains. Longest chain 12 peptides. Score 0.468 Taking the results from Round 3 Chains 25, Residues 154, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6757 restraints for refining 2916 atoms. 6166 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2193 (Rfree = 0.000) for 2916 atoms. Found 13 (13 requested) and removed 29 (6 requested) atoms. Cycle 22: After refmac, R = 0.1943 (Rfree = 0.000) for 2882 atoms. Found 13 (13 requested) and removed 48 (6 requested) atoms. Cycle 23: After refmac, R = 0.2214 (Rfree = 0.000) for 2843 atoms. Found 13 (13 requested) and removed 12 (6 requested) atoms. Cycle 24: After refmac, R = 0.1841 (Rfree = 0.000) for 2832 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. Cycle 25: After refmac, R = 0.1806 (Rfree = 0.000) for 2823 atoms. Found 10 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.81 4.13 Search for helices and strands: 0 residues in 0 chains, 2910 seeds are put forward NCS extension: 8 residues added (0 deleted due to clashes), 2918 seeds are put forward Round 1: 131 peptides, 27 chains. Longest chain 9 peptides. Score 0.277 Round 2: 155 peptides, 28 chains. Longest chain 11 peptides. Score 0.362 Round 3: 149 peptides, 26 chains. Longest chain 12 peptides. Score 0.373 Round 4: 157 peptides, 27 chains. Longest chain 10 peptides. Score 0.388 Round 5: 155 peptides, 25 chains. Longest chain 11 peptides. Score 0.415 Taking the results from Round 5 Chains 25, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 3709 reflections ( 99.52 % complete ) and 7098 restraints for refining 2976 atoms. 6603 conditional restraints added. Observations/parameters ratio is 0.31 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2359 (Rfree = 0.000) for 2976 atoms. Found 14 (14 requested) and removed 25 (7 requested) atoms. Cycle 27: After refmac, R = 0.2422 (Rfree = 0.000) for 2938 atoms. Found 14 (14 requested) and removed 26 (7 requested) atoms. Cycle 28: After refmac, R = 0.2204 (Rfree = 0.000) for 2908 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 29: After refmac, R = 0.2210 (Rfree = 0.000) for 2893 atoms. Found 13 (13 requested) and removed 14 (6 requested) atoms. Cycle 30: After refmac, R = 0.2194 (Rfree = 0.000) for 2881 atoms. Found 13 (13 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.77 4.09 Search for helices and strands: 0 residues in 0 chains, 2981 seeds are put forward NCS extension: 13 residues added (1 deleted due to clashes), 2994 seeds are put forward Round 1: 98 peptides, 21 chains. Longest chain 8 peptides. Score 0.240 Round 2: 129 peptides, 24 chains. Longest chain 8 peptides. Score 0.325 Round 3: 136 peptides, 23 chains. Longest chain 9 peptides. Score 0.373 Round 4: 134 peptides, 23 chains. Longest chain 9 peptides. Score 0.365 Round 5: 132 peptides, 22 chains. Longest chain 9 peptides. Score 0.375 Taking the results from Round 5 Chains 22, Residues 110, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6845 restraints for refining 2907 atoms. 6427 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2291 (Rfree = 0.000) for 2907 atoms. Found 11 (13 requested) and removed 26 (6 requested) atoms. Cycle 32: After refmac, R = 0.1989 (Rfree = 0.000) for 2877 atoms. Found 10 (13 requested) and removed 9 (6 requested) atoms. Cycle 33: After refmac, R = 0.2246 (Rfree = 0.000) for 2863 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 34: After refmac, R = 0.1919 (Rfree = 0.000) for 2850 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. Cycle 35: After refmac, R = 0.2086 (Rfree = 0.000) for 2842 atoms. Found 13 (13 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.79 4.11 Search for helices and strands: 0 residues in 0 chains, 2921 seeds are put forward NCS extension: 0 residues added, 2921 seeds are put forward Round 1: 94 peptides, 22 chains. Longest chain 6 peptides. Score 0.198 Round 2: 128 peptides, 24 chains. Longest chain 11 peptides. Score 0.320 Round 3: 143 peptides, 26 chains. Longest chain 8 peptides. Score 0.348 Round 4: 142 peptides, 25 chains. Longest chain 10 peptides. Score 0.362 Round 5: 133 peptides, 24 chains. Longest chain 13 peptides. Score 0.342 Taking the results from Round 4 Chains 25, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6199 restraints for refining 2723 atoms. 5756 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1846 (Rfree = 0.000) for 2723 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 37: After refmac, R = 0.1896 (Rfree = 0.000) for 2720 atoms. Found 12 (12 requested) and removed 12 (6 requested) atoms. Cycle 38: After refmac, R = 0.1776 (Rfree = 0.000) for 2717 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 39: After refmac, R = 0.1778 (Rfree = 0.000) for 2710 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 40: After refmac, R = 0.1720 (Rfree = 0.000) for 2702 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.82 4.14 Search for helices and strands: 0 residues in 0 chains, 2787 seeds are put forward NCS extension: 0 residues added, 2787 seeds are put forward Round 1: 97 peptides, 21 chains. Longest chain 7 peptides. Score 0.235 Round 2: 127 peptides, 26 chains. Longest chain 9 peptides. Score 0.278 Round 3: 135 peptides, 26 chains. Longest chain 8 peptides. Score 0.313 Round 4: 127 peptides, 23 chains. Longest chain 13 peptides. Score 0.335 Round 5: 144 peptides, 25 chains. Longest chain 13 peptides. Score 0.370 Taking the results from Round 5 Chains 25, Residues 119, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3709 reflections ( 99.52 % complete ) and 6371 restraints for refining 2797 atoms. 5920 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1886 (Rfree = 0.000) for 2797 atoms. Found 13 (13 requested) and removed 22 (6 requested) atoms. Cycle 42: After refmac, R = 0.2183 (Rfree = 0.000) for 2773 atoms. Found 13 (13 requested) and removed 19 (6 requested) atoms. Cycle 43: After refmac, R = 0.1836 (Rfree = 0.000) for 2757 atoms. Found 13 (13 requested) and removed 13 (6 requested) atoms. Cycle 44: After refmac, R = 0.2106 (Rfree = 0.000) for 2746 atoms. Found 13 (13 requested) and removed 17 (6 requested) atoms. Cycle 45: After refmac, R = 0.1712 (Rfree = 0.000) for 2736 atoms. Found 13 (13 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.79 4.11 Search for helices and strands: 0 residues in 0 chains, 2798 seeds are put forward NCS extension: 0 residues added, 2798 seeds are put forward Round 1: 98 peptides, 21 chains. Longest chain 8 peptides. Score 0.240 Round 2: 109 peptides, 20 chains. Longest chain 12 peptides. Score 0.312 Round 3: 120 peptides, 23 chains. Longest chain 8 peptides. Score 0.304 Round 4: 121 peptides, 22 chains. Longest chain 10 peptides. Score 0.327 Round 5: 124 peptides, 21 chains. Longest chain 10 peptides. Score 0.359 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 103, 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 2fur-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3709 reflections ( 99.52 % complete ) and 6361 restraints for refining 2754 atoms. 5970 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1969 (Rfree = 0.000) for 2754 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2088 (Rfree = 0.000) for 2731 atoms. Found 0 (13 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1836 (Rfree = 0.000) for 2713 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1412 (Rfree = 0.000) for 2701 atoms. TimeTaking 50.57