Mon 24 Dec 07:27:01 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkd-3.8-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/1vkd-3.8-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/1vkd-3.8-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.8-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.8-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.8-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:27:05 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/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.8-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/1vkd-3.8-parrot-noncs/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 1613 and 0 Target number of residues in the AU: 1613 Target solvent content: 0.6118 Checking the provided sequence file Detected sequence length: 338 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 2028 Adjusted target solvent content: 0.51 Input MTZ file: 1vkd-3.8-parrot-noncs.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: 86.922 101.512 254.880 90.000 90.000 90.000 Input sequence file: 1vkd-3.8-parrot-noncs.fasta_lf Building free atoms model in initial map for 16224 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: 127.440 3.800 Wilson plot Bfac: 57.67 22890 reflections ( 99.67 % complete ) and 0 restraints for refining 17989 atoms. Observations/parameters ratio is 0.32 ------------------------------------------------------ Starting model: R = 0.3202 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2904 (Rfree = 0.000) for 17989 atoms. Found 98 (98 requested) and removed 124 (49 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.34 3.30 Search for helices and strands: 0 residues in 0 chains, 18151 seeds are put forward NCS extension: 0 residues added, 18151 seeds are put forward Round 1: 760 peptides, 156 chains. Longest chain 11 peptides. Score 0.283 Round 2: 998 peptides, 173 chains. Longest chain 14 peptides. Score 0.407 Round 3: 1100 peptides, 180 chains. Longest chain 15 peptides. Score 0.456 Round 4: 1193 peptides, 187 chains. Longest chain 17 peptides. Score 0.496 Round 5: 1182 peptides, 180 chains. Longest chain 18 peptides. Score 0.508 Taking the results from Round 5 Chains 183, Residues 1002, Estimated correctness of the model 0.0 % 11 chains (64 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 33014 restraints for refining 14669 atoms. 28997 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2294 (Rfree = 0.000) for 14669 atoms. Found 55 (80 requested) and removed 86 (40 requested) atoms. Cycle 2: After refmac, R = 0.2176 (Rfree = 0.000) for 14427 atoms. Found 50 (80 requested) and removed 72 (40 requested) atoms. Cycle 3: After refmac, R = 0.2100 (Rfree = 0.000) for 14329 atoms. Found 36 (79 requested) and removed 72 (39 requested) atoms. Cycle 4: After refmac, R = 0.2015 (Rfree = 0.000) for 14235 atoms. Found 39 (78 requested) and removed 59 (39 requested) atoms. Cycle 5: After refmac, R = 0.1972 (Rfree = 0.000) for 14163 atoms. Found 23 (78 requested) and removed 69 (39 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.33 3.29 Search for helices and strands: 0 residues in 0 chains, 14422 seeds are put forward NCS extension: 23 residues added (3 deleted due to clashes), 14445 seeds are put forward Round 1: 978 peptides, 183 chains. Longest chain 19 peptides. Score 0.363 Round 2: 1124 peptides, 173 chains. Longest chain 17 peptides. Score 0.491 Round 3: 1143 peptides, 170 chains. Longest chain 24 peptides. Score 0.511 Round 4: 1134 peptides, 158 chains. Longest chain 22 peptides. Score 0.538 Round 5: 1161 peptides, 160 chains. Longest chain 21 peptides. Score 0.549 Taking the results from Round 5 Chains 164, Residues 1001, Estimated correctness of the model 0.0 % 12 chains (74 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 33052 restraints for refining 14673 atoms. 29000 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2196 (Rfree = 0.000) for 14673 atoms. Found 56 (80 requested) and removed 100 (40 requested) atoms. Cycle 7: After refmac, R = 0.2131 (Rfree = 0.000) for 14513 atoms. Found 39 (80 requested) and removed 86 (40 requested) atoms. Cycle 8: After refmac, R = 0.2069 (Rfree = 0.000) for 14403 atoms. Found 58 (79 requested) and removed 74 (39 requested) atoms. Cycle 9: After refmac, R = 0.1962 (Rfree = 0.000) for 14350 atoms. Found 37 (79 requested) and removed 66 (39 requested) atoms. Cycle 10: After refmac, R = 0.1761 (Rfree = 0.000) for 14280 atoms. Found 14 (78 requested) and removed 64 (39 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 14475 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 14497 seeds are put forward Round 1: 990 peptides, 186 chains. Longest chain 13 peptides. Score 0.362 Round 2: 1098 peptides, 166 chains. Longest chain 24 peptides. Score 0.494 Round 3: 1120 peptides, 161 chains. Longest chain 17 peptides. Score 0.522 Round 4: 1150 peptides, 167 chains. Longest chain 26 peptides. Score 0.524 Round 5: 1160 peptides, 171 chains. Longest chain 18 peptides. Score 0.519 Taking the results from Round 4 Chains 173, Residues 983, Estimated correctness of the model 0.0 % 11 chains (89 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 32679 restraints for refining 14675 atoms. 28604 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2166 (Rfree = 0.000) for 14675 atoms. Found 61 (80 requested) and removed 95 (40 requested) atoms. Cycle 12: After refmac, R = 0.1957 (Rfree = 0.000) for 14558 atoms. Found 24 (80 requested) and removed 73 (40 requested) atoms. Cycle 13: After refmac, R = 0.1921 (Rfree = 0.000) for 14469 atoms. Found 30 (79 requested) and removed 67 (39 requested) atoms. Cycle 14: After refmac, R = 0.1832 (Rfree = 0.000) for 14406 atoms. Found 21 (79 requested) and removed 58 (39 requested) atoms. Cycle 15: After refmac, R = 0.1836 (Rfree = 0.000) for 14342 atoms. Found 23 (79 requested) and removed 60 (39 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.36 3.32 Search for helices and strands: 0 residues in 0 chains, 14560 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 14573 seeds are put forward Round 1: 966 peptides, 179 chains. Longest chain 14 peptides. Score 0.366 Round 2: 1052 peptides, 163 chains. Longest chain 18 peptides. Score 0.473 Round 3: 1081 peptides, 159 chains. Longest chain 20 peptides. Score 0.503 Round 4: 1102 peptides, 156 chains. Longest chain 24 peptides. Score 0.524 Round 5: 1078 peptides, 160 chains. Longest chain 17 peptides. Score 0.498 Taking the results from Round 4 Chains 160, Residues 946, Estimated correctness of the model 0.0 % 8 chains (53 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 22890 reflections ( 99.67 % complete ) and 33435 restraints for refining 14674 atoms. 29656 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2108 (Rfree = 0.000) for 14674 atoms. Found 55 (80 requested) and removed 76 (40 requested) atoms. Cycle 17: After refmac, R = 0.1944 (Rfree = 0.000) for 14587 atoms. Found 24 (80 requested) and removed 62 (40 requested) atoms. Cycle 18: After refmac, R = 0.1862 (Rfree = 0.000) for 14505 atoms. Found 20 (80 requested) and removed 58 (40 requested) atoms. Cycle 19: After refmac, R = 0.1775 (Rfree = 0.000) for 14447 atoms. Found 18 (79 requested) and removed 46 (39 requested) atoms. Cycle 20: After refmac, R = 0.1752 (Rfree = 0.000) for 14397 atoms. Found 19 (79 requested) and removed 51 (39 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 14600 seeds are put forward NCS extension: 14 residues added (2 deleted due to clashes), 14614 seeds are put forward Round 1: 980 peptides, 183 chains. Longest chain 20 peptides. Score 0.364 Round 2: 1049 peptides, 159 chains. Longest chain 20 peptides. Score 0.483 Round 3: 1068 peptides, 160 chains. Longest chain 19 peptides. Score 0.492 Round 4: 1079 peptides, 164 chains. Longest chain 22 peptides. Score 0.488 Round 5: 1104 peptides, 160 chains. Longest chain 21 peptides. Score 0.514 Taking the results from Round 5 Chains 163, Residues 944, Estimated correctness of the model 0.0 % 9 chains (51 residues) have been docked in sequence ------------------------------------------------------ Failed to save intermediate PDB 22890 reflections ( 99.67 % complete ) and 33616 restraints for refining 14674 atoms. 29841 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2087 (Rfree = 0.000) for 14674 atoms. Found 43 (80 requested) and removed 75 (40 requested) atoms. Cycle 22: After refmac, R = 0.1974 (Rfree = 0.000) for 14567 atoms. Found 26 (80 requested) and removed 59 (40 requested) atoms. Cycle 23: After refmac, R = 0.1967 (Rfree = 0.000) for 14488 atoms. Found 31 (79 requested) and removed 57 (39 requested) atoms. Cycle 24: After refmac, R = 0.1922 (Rfree = 0.000) for 14439 atoms. Found 20 (79 requested) and removed 54 (39 requested) atoms. Cycle 25: After refmac, R = 0.1859 (Rfree = 0.000) for 14380 atoms. Found 23 (79 requested) and removed 54 (39 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 14591 seeds are put forward NCS extension: 25 residues added (1 deleted due to clashes), 14616 seeds are put forward Round 1: 924 peptides, 179 chains. Longest chain 12 peptides. Score 0.335 Round 2: 1003 peptides, 160 chains. Longest chain 20 peptides. Score 0.449 Round 3: 1030 peptides, 166 chains. Longest chain 19 peptides. Score 0.450 Round 4: 1057 peptides, 161 chains. Longest chain 17 peptides. Score 0.482 Round 5: 1038 peptides, 162 chains. Longest chain 22 peptides. Score 0.467 Taking the results from Round 4 Chains 163, Residues 896, Estimated correctness of the model 0.0 % 7 chains (50 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 33778 restraints for refining 14672 atoms. 30181 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2095 (Rfree = 0.000) for 14672 atoms. Found 51 (80 requested) and removed 71 (40 requested) atoms. Cycle 27: After refmac, R = 0.2011 (Rfree = 0.000) for 14585 atoms. Found 37 (80 requested) and removed 69 (40 requested) atoms. Failed to save intermediate PDB Cycle 28: After refmac, R = 0.2019 (Rfree = 0.000) for 14514 atoms. Found 44 (80 requested) and removed 69 (40 requested) atoms. Cycle 29: After refmac, R = 0.1946 (Rfree = 0.000) for 14454 atoms. Found 33 (79 requested) and removed 63 (39 requested) atoms. Cycle 30: After refmac, R = 0.1757 (Rfree = 0.000) for 14398 atoms. Found 11 (79 requested) and removed 48 (39 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 14577 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 14596 seeds are put forward Round 1: 892 peptides, 175 chains. Longest chain 15 peptides. Score 0.324 Round 2: 977 peptides, 170 chains. Longest chain 17 peptides. Score 0.402 Round 3: 1021 peptides, 162 chains. Longest chain 20 peptides. Score 0.456 Round 4: 988 peptides, 157 chains. Longest chain 24 peptides. Score 0.448 Round 5: 1023 peptides, 156 chains. Longest chain 28 peptides. Score 0.474 Taking the results from Round 5 Chains 159, Residues 867, Estimated correctness of the model 0.0 % 7 chains (55 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 33816 restraints for refining 14675 atoms. 30284 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2096 (Rfree = 0.000) for 14675 atoms. Found 51 (80 requested) and removed 72 (40 requested) atoms. Cycle 32: After refmac, R = 0.1941 (Rfree = 0.000) for 14583 atoms. Found 33 (80 requested) and removed 59 (40 requested) atoms. Cycle 33: After refmac, R = 0.1910 (Rfree = 0.000) for 14526 atoms. Found 31 (80 requested) and removed 60 (40 requested) atoms. Cycle 34: After refmac, R = 0.1835 (Rfree = 0.000) for 14475 atoms. Found 22 (79 requested) and removed 47 (39 requested) atoms. Cycle 35: After refmac, R = 0.1821 (Rfree = 0.000) for 14433 atoms. Found 14 (79 requested) and removed 41 (39 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.38 3.34 Search for helices and strands: 0 residues in 0 chains, 14625 seeds are put forward NCS extension: 24 residues added (1 deleted due to clashes), 14649 seeds are put forward Round 1: 818 peptides, 168 chains. Longest chain 10 peptides. Score 0.289 Round 2: 900 peptides, 157 chains. Longest chain 14 peptides. Score 0.387 Round 3: 889 peptides, 150 chains. Longest chain 14 peptides. Score 0.401 Round 4: 923 peptides, 154 chains. Longest chain 14 peptides. Score 0.412 Round 5: 960 peptides, 153 chains. Longest chain 17 peptides. Score 0.441 Taking the results from Round 5 Chains 153, Residues 807, Estimated correctness of the model 0.0 % 6 chains (36 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 34365 restraints for refining 14675 atoms. 31190 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2057 (Rfree = 0.000) for 14675 atoms. Found 51 (80 requested) and removed 57 (40 requested) atoms. Cycle 37: After refmac, R = 0.1919 (Rfree = 0.000) for 14636 atoms. Found 23 (80 requested) and removed 68 (40 requested) atoms. Cycle 38: After refmac, R = 0.1872 (Rfree = 0.000) for 14571 atoms. Found 21 (80 requested) and removed 57 (40 requested) atoms. Cycle 39: After refmac, R = 0.1810 (Rfree = 0.000) for 14518 atoms. Found 10 (79 requested) and removed 53 (39 requested) atoms. Cycle 40: After refmac, R = 0.1801 (Rfree = 0.000) for 14457 atoms. Found 28 (79 requested) and removed 56 (39 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.39 3.35 Search for helices and strands: 0 residues in 0 chains, 14654 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 14674 seeds are put forward Round 1: 769 peptides, 155 chains. Longest chain 13 peptides. Score 0.293 Round 2: 849 peptides, 142 chains. Longest chain 18 peptides. Score 0.397 Round 3: 883 peptides, 149 chains. Longest chain 18 peptides. Score 0.399 Round 4: 894 peptides, 139 chains. Longest chain 16 peptides. Score 0.438 Round 5: 906 peptides, 145 chains. Longest chain 16 peptides. Score 0.428 Taking the results from Round 4 Chains 141, Residues 755, Estimated correctness of the model 0.0 % 7 chains (50 residues) have been docked in sequence ------------------------------------------------------ 22890 reflections ( 99.67 % complete ) and 34130 restraints for refining 14675 atoms. 31077 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1959 (Rfree = 0.000) for 14675 atoms. Found 43 (80 requested) and removed 62 (40 requested) atoms. Cycle 42: After refmac, R = 0.1845 (Rfree = 0.000) for 14617 atoms. Found 23 (80 requested) and removed 56 (40 requested) atoms. Cycle 43: After refmac, R = 0.1782 (Rfree = 0.000) for 14565 atoms. Found 19 (80 requested) and removed 47 (40 requested) atoms. Cycle 44: After refmac, R = 0.1744 (Rfree = 0.000) for 14518 atoms. Found 11 (79 requested) and removed 52 (39 requested) atoms. Cycle 45: After refmac, R = 0.1732 (Rfree = 0.000) for 14463 atoms. Found 11 (79 requested) and removed 53 (39 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.40 3.36 Search for helices and strands: 0 residues in 0 chains, 14615 seeds are put forward NCS extension: 28 residues added (3 deleted due to clashes), 14643 seeds are put forward Round 1: 771 peptides, 154 chains. Longest chain 12 peptides. Score 0.298 Round 2: 844 peptides, 142 chains. Longest chain 16 peptides. Score 0.393 Round 3: 874 peptides, 137 chains. Longest chain 17 peptides. Score 0.430 Round 4: 879 peptides, 134 chains. Longest chain 19 peptides. Score 0.443 Round 5: 876 peptides, 135 chains. Longest chain 19 peptides. Score 0.438 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 134, Residues 745, Estimated correctness of the model 0.0 % 4 chains (19 residues) have been docked in sequence Sequence coverage is 2 % Consider running further cycles of model building using 1vkd-3_warpNtrace.pdb as input Building loops using Loopy2018 134 chains (745 residues) following loop building 4 chains (19 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 22890 reflections ( 99.67 % complete ) and 34629 restraints for refining 14674 atoms. 31729 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1894 (Rfree = 0.000) for 14674 atoms. Found 0 (80 requested) and removed 40 (40 requested) atoms. Cycle 47: After refmac, R = 0.1781 (Rfree = 0.000) for 14599 atoms. Found 0 (80 requested) and removed 40 (40 requested) atoms. Cycle 48: After refmac, R = 0.1733 (Rfree = 0.000) for 14540 atoms. Found 0 (80 requested) and removed 40 (40 requested) atoms. Failed to save intermediate PDB Cycle 49: After refmac, R = 0.1687 (Rfree = 0.000) for 14493 atoms. TimeTaking 151.72