Sun 23 Dec 22:22:49 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 2ash-3.2-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ash-3.2-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ash-3.2-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-3.2-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/2ash-3.2-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-3.2-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 22:22:59 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/2ash-3.2-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ash-3.2-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 1160 and 0 Target number of residues in the AU: 1160 Target solvent content: 0.6429 Checking the provided sequence file Detected sequence length: 381 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 1524 Adjusted target solvent content: 0.53 Input MTZ file: 2ash-3.2-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: 5 Cell parameters: 170.109 99.745 124.866 90.000 123.929 90.000 Input sequence file: 2ash-3.2-parrot-hancs.fasta_lf Building free atoms model in initial map for 12192 target number of atoms Had to go as low as 0.85 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: 103.605 3.200 Wilson plot Bfac: 73.62 28706 reflections ( 99.82 % complete ) and 0 restraints for refining 13621 atoms. Observations/parameters ratio is 0.53 ------------------------------------------------------ Starting model: R = 0.3297 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2758 (Rfree = 0.000) for 13621 atoms. Found 122 (122 requested) and removed 109 (61 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 13889 seeds are put forward NCS extension: 0 residues added, 13889 seeds are put forward Round 1: 743 peptides, 134 chains. Longest chain 14 peptides. Score 0.378 Round 2: 893 peptides, 131 chains. Longest chain 22 peptides. Score 0.518 Round 3: 954 peptides, 124 chains. Longest chain 22 peptides. Score 0.585 Round 4: 973 peptides, 123 chains. Longest chain 24 peptides. Score 0.602 Round 5: 965 peptides, 122 chains. Longest chain 23 peptides. Score 0.599 Taking the results from Round 4 Chains 126, Residues 850, Estimated correctness of the model 41.6 % 9 chains (105 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 23565 restraints for refining 11129 atoms. 19907 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2534 (Rfree = 0.000) for 11129 atoms. Found 89 (99 requested) and removed 69 (49 requested) atoms. Cycle 2: After refmac, R = 0.2354 (Rfree = 0.000) for 11005 atoms. Found 37 (100 requested) and removed 54 (50 requested) atoms. Cycle 3: After refmac, R = 0.2325 (Rfree = 0.000) for 10923 atoms. Found 42 (98 requested) and removed 57 (49 requested) atoms. Cycle 4: After refmac, R = 0.2278 (Rfree = 0.000) for 10870 atoms. Found 28 (97 requested) and removed 56 (48 requested) atoms. Cycle 5: After refmac, R = 0.2239 (Rfree = 0.000) for 10813 atoms. Found 34 (97 requested) and removed 50 (48 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.26 3.13 Search for helices and strands: 0 residues in 0 chains, 11179 seeds are put forward NCS extension: 19 residues added (3 deleted due to clashes), 11198 seeds are put forward Round 1: 852 peptides, 125 chains. Longest chain 23 peptides. Score 0.506 Round 2: 928 peptides, 120 chains. Longest chain 21 peptides. Score 0.580 Round 3: 965 peptides, 114 chains. Longest chain 31 peptides. Score 0.623 Round 4: 981 peptides, 119 chains. Longest chain 37 peptides. Score 0.619 Round 5: 967 peptides, 123 chains. Longest chain 26 peptides. Score 0.597 Taking the results from Round 3 Chains 120, Residues 851, Estimated correctness of the model 47.1 % 7 chains (100 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 23853 restraints for refining 11127 atoms. 20172 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2419 (Rfree = 0.000) for 11127 atoms. Found 75 (99 requested) and removed 64 (49 requested) atoms. Cycle 7: After refmac, R = 0.2258 (Rfree = 0.000) for 11087 atoms. Found 38 (99 requested) and removed 60 (49 requested) atoms. Cycle 8: After refmac, R = 0.2213 (Rfree = 0.000) for 11033 atoms. Found 30 (99 requested) and removed 55 (49 requested) atoms. Cycle 9: After refmac, R = 0.2147 (Rfree = 0.000) for 10982 atoms. Found 34 (98 requested) and removed 50 (49 requested) atoms. Cycle 10: After refmac, R = 0.2093 (Rfree = 0.000) for 10953 atoms. Found 19 (98 requested) and removed 51 (49 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.25 3.12 Search for helices and strands provided no result - WARNING Search for helices and strands: 0 residues in 0 chains, 11298 seeds are put forward NCS extension: 9 residues added (13 deleted due to clashes), 11307 seeds are put forward Round 1: 854 peptides, 125 chains. Longest chain 20 peptides. Score 0.508 Round 2: 936 peptides, 109 chains. Longest chain 40 peptides. Score 0.619 Round 3: 928 peptides, 107 chains. Longest chain 31 peptides. Score 0.620 Round 4: 962 peptides, 106 chains. Longest chain 42 peptides. Score 0.645 Round 5: 951 peptides, 108 chains. Longest chain 28 peptides. Score 0.632 Taking the results from Round 4 Chains 111, Residues 856, Estimated correctness of the model 52.6 % 8 chains (142 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 23251 restraints for refining 11126 atoms. 19374 conditional restraints added. Observations/parameters ratio is 0.65 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2413 (Rfree = 0.000) for 11126 atoms. Found 75 (99 requested) and removed 85 (49 requested) atoms. Cycle 12: After refmac, R = 0.2227 (Rfree = 0.000) for 11085 atoms. Found 28 (99 requested) and removed 53 (49 requested) atoms. Cycle 13: After refmac, R = 0.2183 (Rfree = 0.000) for 11038 atoms. Found 34 (99 requested) and removed 49 (49 requested) atoms. Cycle 14: After refmac, R = 0.2155 (Rfree = 0.000) for 11009 atoms. Found 20 (98 requested) and removed 49 (49 requested) atoms. Cycle 15: After refmac, R = 0.2116 (Rfree = 0.000) for 10963 atoms. Found 16 (98 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.26 3.13 Search for helices and strands: 0 residues in 0 chains, 11313 seeds are put forward NCS extension: 19 residues added (11 deleted due to clashes), 11332 seeds are put forward Round 1: 847 peptides, 123 chains. Longest chain 31 peptides. Score 0.509 Round 2: 912 peptides, 111 chains. Longest chain 33 peptides. Score 0.597 Round 3: 954 peptides, 105 chains. Longest chain 34 peptides. Score 0.642 Round 4: 984 peptides, 105 chains. Longest chain 32 peptides. Score 0.661 Round 5: 969 peptides, 117 chains. Longest chain 24 peptides. Score 0.617 Taking the results from Round 4 Chains 116, Residues 879, Estimated correctness of the model 56.5 % 10 chains (150 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 22625 restraints for refining 11129 atoms. 18618 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2333 (Rfree = 0.000) for 11129 atoms. Found 81 (99 requested) and removed 67 (49 requested) atoms. Cycle 17: After refmac, R = 0.2141 (Rfree = 0.000) for 11116 atoms. Found 32 (100 requested) and removed 54 (50 requested) atoms. Cycle 18: After refmac, R = 0.2089 (Rfree = 0.000) for 11074 atoms. Found 21 (99 requested) and removed 49 (49 requested) atoms. Cycle 19: After refmac, R = 0.2066 (Rfree = 0.000) for 11036 atoms. Found 20 (99 requested) and removed 50 (49 requested) atoms. Cycle 20: After refmac, R = 0.2035 (Rfree = 0.000) for 10999 atoms. Found 21 (98 requested) and removed 50 (49 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 11317 seeds are put forward NCS extension: 21 residues added (19 deleted due to clashes), 11338 seeds are put forward Round 1: 893 peptides, 129 chains. Longest chain 30 peptides. Score 0.524 Round 2: 910 peptides, 107 chains. Longest chain 32 peptides. Score 0.608 Round 3: 914 peptides, 99 chains. Longest chain 28 peptides. Score 0.635 Round 4: 942 peptides, 104 chains. Longest chain 34 peptides. Score 0.638 Round 5: 907 peptides, 103 chains. Longest chain 34 peptides. Score 0.618 Taking the results from Round 4 Chains 111, Residues 838, Estimated correctness of the model 50.9 % 7 chains (109 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 23704 restraints for refining 11131 atoms. 20004 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2271 (Rfree = 0.000) for 11131 atoms. Found 69 (99 requested) and removed 67 (49 requested) atoms. Cycle 22: After refmac, R = 0.2129 (Rfree = 0.000) for 11096 atoms. Found 36 (99 requested) and removed 51 (49 requested) atoms. Cycle 23: After refmac, R = 0.2113 (Rfree = 0.000) for 11070 atoms. Found 30 (99 requested) and removed 49 (49 requested) atoms. Cycle 24: After refmac, R = 0.2089 (Rfree = 0.000) for 11037 atoms. Found 27 (99 requested) and removed 50 (49 requested) atoms. Cycle 25: After refmac, R = 0.2059 (Rfree = 0.000) for 11004 atoms. Found 29 (98 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.27 3.14 Search for helices and strands: 0 residues in 0 chains, 11326 seeds are put forward NCS extension: 11 residues added (10 deleted due to clashes), 11337 seeds are put forward Round 1: 840 peptides, 115 chains. Longest chain 29 peptides. Score 0.531 Round 2: 910 peptides, 108 chains. Longest chain 31 peptides. Score 0.605 Round 3: 929 peptides, 103 chains. Longest chain 31 peptides. Score 0.633 Round 4: 912 peptides, 110 chains. Longest chain 28 peptides. Score 0.600 Round 5: 924 peptides, 110 chains. Longest chain 28 peptides. Score 0.608 Taking the results from Round 3 Chains 113, Residues 826, Estimated correctness of the model 49.7 % 9 chains (132 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 23511 restraints for refining 11129 atoms. 19767 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2345 (Rfree = 0.000) for 11129 atoms. Found 84 (99 requested) and removed 66 (49 requested) atoms. Cycle 27: After refmac, R = 0.2192 (Rfree = 0.000) for 11121 atoms. Found 39 (100 requested) and removed 55 (50 requested) atoms. Cycle 28: After refmac, R = 0.2174 (Rfree = 0.000) for 11092 atoms. Found 32 (99 requested) and removed 51 (49 requested) atoms. Cycle 29: After refmac, R = 0.2141 (Rfree = 0.000) for 11061 atoms. Found 33 (99 requested) and removed 49 (49 requested) atoms. Cycle 30: After refmac, R = 0.2107 (Rfree = 0.000) for 11033 atoms. Found 25 (99 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.25 3.12 Search for helices and strands: 0 residues in 0 chains, 11344 seeds are put forward NCS extension: 15 residues added (7 deleted due to clashes), 11359 seeds are put forward Round 1: 754 peptides, 106 chains. Longest chain 24 peptides. Score 0.495 Round 2: 835 peptides, 101 chains. Longest chain 28 peptides. Score 0.575 Round 3: 845 peptides, 97 chains. Longest chain 35 peptides. Score 0.595 Round 4: 836 peptides, 97 chains. Longest chain 35 peptides. Score 0.589 Round 5: 839 peptides, 99 chains. Longest chain 23 peptides. Score 0.584 Taking the results from Round 3 Chains 100, Residues 748, Estimated correctness of the model 39.7 % 5 chains (71 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 24773 restraints for refining 11131 atoms. 21614 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2279 (Rfree = 0.000) for 11131 atoms. Found 54 (99 requested) and removed 54 (49 requested) atoms. Cycle 32: After refmac, R = 0.2186 (Rfree = 0.000) for 11108 atoms. Found 35 (99 requested) and removed 50 (49 requested) atoms. Cycle 33: After refmac, R = 0.2137 (Rfree = 0.000) for 11079 atoms. Found 17 (99 requested) and removed 49 (49 requested) atoms. Cycle 34: After refmac, R = 0.2123 (Rfree = 0.000) for 11038 atoms. Found 24 (99 requested) and removed 49 (49 requested) atoms. Cycle 35: After refmac, R = 0.2068 (Rfree = 0.000) for 11004 atoms. Found 24 (98 requested) and removed 50 (49 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.26 3.13 Search for helices and strands: 0 residues in 0 chains, 11322 seeds are put forward NCS extension: 11 residues added (7 deleted due to clashes), 11333 seeds are put forward Round 1: 764 peptides, 113 chains. Longest chain 26 peptides. Score 0.477 Round 2: 800 peptides, 105 chains. Longest chain 29 peptides. Score 0.535 Round 3: 804 peptides, 95 chains. Longest chain 31 peptides. Score 0.572 Round 4: 782 peptides, 97 chains. Longest chain 25 peptides. Score 0.549 Round 5: 815 peptides, 101 chains. Longest chain 25 peptides. Score 0.560 Taking the results from Round 3 Chains 102, Residues 709, Estimated correctness of the model 33.3 % 9 chains (111 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 24511 restraints for refining 11130 atoms. 21363 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2247 (Rfree = 0.000) for 11130 atoms. Found 67 (99 requested) and removed 61 (49 requested) atoms. Cycle 37: After refmac, R = 0.2158 (Rfree = 0.000) for 11110 atoms. Found 28 (99 requested) and removed 49 (49 requested) atoms. Cycle 38: After refmac, R = 0.2155 (Rfree = 0.000) for 11073 atoms. Found 32 (99 requested) and removed 49 (49 requested) atoms. Cycle 39: After refmac, R = 0.2072 (Rfree = 0.000) for 11046 atoms. Found 25 (99 requested) and removed 49 (49 requested) atoms. Cycle 40: After refmac, R = 0.2054 (Rfree = 0.000) for 11015 atoms. Found 23 (98 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.26 3.13 Search for helices and strands: 0 residues in 0 chains, 11359 seeds are put forward NCS extension: 41 residues added (0 deleted due to clashes), 11400 seeds are put forward Round 1: 749 peptides, 116 chains. Longest chain 24 peptides. Score 0.454 Round 2: 797 peptides, 104 chains. Longest chain 26 peptides. Score 0.536 Round 3: 806 peptides, 103 chains. Longest chain 28 peptides. Score 0.547 Round 4: 809 peptides, 102 chains. Longest chain 29 peptides. Score 0.552 Round 5: 830 peptides, 103 chains. Longest chain 29 peptides. Score 0.565 Taking the results from Round 5 Chains 113, Residues 727, Estimated correctness of the model 31.3 % 9 chains (110 residues) have been docked in sequence ------------------------------------------------------ 28706 reflections ( 99.82 % complete ) and 24046 restraints for refining 11129 atoms. 20804 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2244 (Rfree = 0.000) for 11129 atoms. Found 67 (99 requested) and removed 60 (49 requested) atoms. Cycle 42: After refmac, R = 0.2082 (Rfree = 0.000) for 11108 atoms. Found 24 (99 requested) and removed 49 (49 requested) atoms. Cycle 43: After refmac, R = 0.2066 (Rfree = 0.000) for 11066 atoms. Found 35 (99 requested) and removed 49 (49 requested) atoms. Cycle 44: After refmac, R = 0.2030 (Rfree = 0.000) for 11046 atoms. Found 25 (99 requested) and removed 49 (49 requested) atoms. Failed to save intermediate PDB Cycle 45: After refmac, R = 0.1979 (Rfree = 0.000) for 11014 atoms. Found 16 (98 requested) and removed 49 (49 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.13 Search for helices and strands: 0 residues in 0 chains, 11348 seeds are put forward NCS extension: 22 residues added (2 deleted due to clashes), 11370 seeds are put forward Round 1: 694 peptides, 116 chains. Longest chain 19 peptides. Score 0.405 Round 2: 753 peptides, 101 chains. Longest chain 27 peptides. Score 0.512 Round 3: 757 peptides, 105 chains. Longest chain 22 peptides. Score 0.501 Round 4: 782 peptides, 103 chains. Longest chain 27 peptides. Score 0.528 Round 5: 806 peptides, 106 chains. Longest chain 25 peptides. Score 0.536 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 112, Residues 700, Estimated correctness of the model 22.7 % 8 chains (80 residues) have been docked in sequence Sequence coverage is 11 % Consider running further cycles of model building using 2ash-3_warpNtrace.pdb as input Building loops using Loopy2018 112 chains (700 residues) following loop building 8 chains (80 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 28706 reflections ( 99.82 % complete ) and 24896 restraints for refining 11131 atoms. 21922 conditional restraints added. Observations/parameters ratio is 0.64 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2209 (Rfree = 0.000) for 11131 atoms. Found 0 (99 requested) and removed 49 (49 requested) atoms. Cycle 47: After refmac, R = 0.2143 (Rfree = 0.000) for 11055 atoms. Found 0 (99 requested) and removed 19 (49 requested) atoms. Cycle 48: After refmac, R = 0.2103 (Rfree = 0.000) for 11029 atoms. Found 0 (99 requested) and removed 13 (49 requested) atoms. Cycle 49: After refmac, R = 0.2056 (Rfree = 0.000) for 11015 atoms. TimeTaking 136.97