null 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 2prx-2.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2prx-2.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2prx-2.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-2.0-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/2prx-2.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-2.0-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 22:22:59 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/2prx-2.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2prx-2.0-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 296 and 0 Target number of residues in the AU: 296 Target solvent content: 0.4551 Checking the provided sequence file Detected sequence length: 160 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 320 Adjusted target solvent content: 0.41 Input MTZ file: 2prx-2.0-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: 144 Cell parameters: 38.520 38.520 171.590 90.000 90.000 120.000 Input sequence file: 2prx-2.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2560 target number of atoms Had to go as low as 0.60 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 1 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: 28.816 2.000 Wilson plot Bfac: 15.36 19184 reflections ( 99.72 % complete ) and 0 restraints for refining 2841 atoms. Observations/parameters ratio is 1.69 ------------------------------------------------------ Starting model: R = 0.3423 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3057 (Rfree = 0.000) for 2841 atoms. Found 74 (97 requested) and removed 56 (48 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.86 2.10 NCS extension: 0 residues added, 2859 seeds are put forward Round 1: 132 peptides, 26 chains. Longest chain 9 peptides. Score 0.337 Round 2: 158 peptides, 26 chains. Longest chain 13 peptides. Score 0.474 Round 3: 181 peptides, 23 chains. Longest chain 19 peptides. Score 0.631 Round 4: 184 peptides, 23 chains. Longest chain 23 peptides. Score 0.642 Round 5: 174 peptides, 21 chains. Longest chain 18 peptides. Score 0.638 Taking the results from Round 4 Chains 24, Residues 161, Estimated correctness of the model 89.2 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 4778 restraints for refining 2482 atoms. 4114 conditional restraints added. Observations/parameters ratio is 1.93 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3138 (Rfree = 0.000) for 2482 atoms. Found 64 (85 requested) and removed 42 (42 requested) atoms. Cycle 2: After refmac, R = 0.2900 (Rfree = 0.000) for 2503 atoms. Found 58 (85 requested) and removed 22 (42 requested) atoms. Cycle 3: After refmac, R = 0.2716 (Rfree = 0.000) for 2538 atoms. Found 47 (86 requested) and removed 11 (43 requested) atoms. Cycle 4: After refmac, R = 0.2552 (Rfree = 0.000) for 2572 atoms. Found 58 (88 requested) and removed 12 (44 requested) atoms. Cycle 5: After refmac, R = 0.2449 (Rfree = 0.000) for 2618 atoms. Found 51 (89 requested) and removed 10 (44 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.81 2.04 NCS extension: 8 residues added (6 deleted due to clashes), 2686 seeds are put forward Round 1: 172 peptides, 25 chains. Longest chain 17 peptides. Score 0.559 Round 2: 188 peptides, 21 chains. Longest chain 26 peptides. Score 0.687 Round 3: 191 peptides, 22 chains. Longest chain 20 peptides. Score 0.682 Round 4: 189 peptides, 23 chains. Longest chain 20 peptides. Score 0.660 Round 5: 189 peptides, 23 chains. Longest chain 20 peptides. Score 0.660 Taking the results from Round 2 Chains 23, Residues 167, Estimated correctness of the model 91.5 % 2 chains (27 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 4948 restraints for refining 2591 atoms. 4225 conditional restraints added. Observations/parameters ratio is 1.85 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2595 (Rfree = 0.000) for 2591 atoms. Found 70 (88 requested) and removed 27 (44 requested) atoms. Cycle 7: After refmac, R = 0.2453 (Rfree = 0.000) for 2633 atoms. Found 55 (90 requested) and removed 13 (45 requested) atoms. Cycle 8: After refmac, R = 0.2367 (Rfree = 0.000) for 2674 atoms. Found 54 (91 requested) and removed 6 (45 requested) atoms. Cycle 9: After refmac, R = 0.2296 (Rfree = 0.000) for 2721 atoms. Found 46 (93 requested) and removed 8 (46 requested) atoms. Cycle 10: After refmac, R = 0.2232 (Rfree = 0.000) for 2758 atoms. Found 41 (94 requested) and removed 7 (47 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.80 2.03 NCS extension: 9 residues added (8 deleted due to clashes), 2805 seeds are put forward Round 1: 165 peptides, 20 chains. Longest chain 20 peptides. Score 0.621 Round 2: 170 peptides, 19 chains. Longest chain 24 peptides. Score 0.657 Round 3: 164 peptides, 18 chains. Longest chain 20 peptides. Score 0.652 Round 4: 168 peptides, 18 chains. Longest chain 20 peptides. Score 0.666 Round 5: 166 peptides, 19 chains. Longest chain 20 peptides. Score 0.642 Taking the results from Round 4 Chains 18, Residues 150, Estimated correctness of the model 90.5 % 1 chains (18 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 5218 restraints for refining 2683 atoms. 4589 conditional restraints added. Observations/parameters ratio is 1.79 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2369 (Rfree = 0.000) for 2683 atoms. Found 86 (91 requested) and removed 15 (45 requested) atoms. Cycle 12: After refmac, R = 0.2236 (Rfree = 0.000) for 2754 atoms. Found 70 (94 requested) and removed 6 (47 requested) atoms. Cycle 13: After refmac, R = 0.2147 (Rfree = 0.000) for 2818 atoms. Found 55 (96 requested) and removed 7 (48 requested) atoms. Cycle 14: After refmac, R = 0.2086 (Rfree = 0.000) for 2865 atoms. Found 42 (98 requested) and removed 17 (49 requested) atoms. Cycle 15: After refmac, R = 0.2025 (Rfree = 0.000) for 2890 atoms. Found 48 (99 requested) and removed 11 (49 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.80 2.03 NCS extension: 15 residues added (2 deleted due to clashes), 2950 seeds are put forward Round 1: 166 peptides, 20 chains. Longest chain 18 peptides. Score 0.625 Round 2: 166 peptides, 18 chains. Longest chain 20 peptides. Score 0.659 Round 3: 167 peptides, 17 chains. Longest chain 21 peptides. Score 0.679 Round 4: 176 peptides, 21 chains. Longest chain 21 peptides. Score 0.646 Round 5: 171 peptides, 18 chains. Longest chain 22 peptides. Score 0.677 Taking the results from Round 3 Chains 17, Residues 150, Estimated correctness of the model 91.1 % 1 chains (17 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 5584 restraints for refining 2835 atoms. 4955 conditional restraints added. Observations/parameters ratio is 1.69 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2208 (Rfree = 0.000) for 2835 atoms. Found 92 (97 requested) and removed 16 (48 requested) atoms. Cycle 17: After refmac, R = 0.2060 (Rfree = 0.000) for 2911 atoms. Found 63 (99 requested) and removed 9 (49 requested) atoms. Cycle 18: After refmac, R = 0.1978 (Rfree = 0.000) for 2964 atoms. Found 45 (101 requested) and removed 10 (50 requested) atoms. Cycle 19: After refmac, R = 0.1927 (Rfree = 0.000) for 2998 atoms. Found 48 (102 requested) and removed 7 (51 requested) atoms. Cycle 20: After refmac, R = 0.1879 (Rfree = 0.000) for 3038 atoms. Found 31 (104 requested) and removed 8 (52 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.81 2.04 NCS extension: 15 residues added (2 deleted due to clashes), 3080 seeds are put forward Round 1: 164 peptides, 22 chains. Longest chain 18 peptides. Score 0.581 Round 2: 170 peptides, 20 chains. Longest chain 23 peptides. Score 0.640 Round 3: 172 peptides, 21 chains. Longest chain 20 peptides. Score 0.631 Round 4: 163 peptides, 19 chains. Longest chain 19 peptides. Score 0.631 Round 5: 159 peptides, 21 chains. Longest chain 22 peptides. Score 0.579 Taking the results from Round 2 Chains 22, Residues 150, Estimated correctness of the model 89.1 % 2 chains (29 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 5675 restraints for refining 2949 atoms. 4990 conditional restraints added. Observations/parameters ratio is 1.63 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2146 (Rfree = 0.000) for 2949 atoms. Found 101 (101 requested) and removed 34 (50 requested) atoms. Cycle 22: After refmac, R = 0.1987 (Rfree = 0.000) for 3016 atoms. Found 73 (103 requested) and removed 8 (51 requested) atoms. Cycle 23: After refmac, R = 0.1917 (Rfree = 0.000) for 3078 atoms. Found 43 (105 requested) and removed 12 (52 requested) atoms. Cycle 24: After refmac, R = 0.1844 (Rfree = 0.000) for 3106 atoms. Found 50 (106 requested) and removed 8 (53 requested) atoms. Cycle 25: After refmac, R = 0.1819 (Rfree = 0.000) for 3146 atoms. Found 41 (107 requested) and removed 21 (53 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.80 2.03 NCS extension: 7 residues added (4 deleted due to clashes), 3181 seeds are put forward Round 1: 150 peptides, 18 chains. Longest chain 18 peptides. Score 0.598 Round 2: 152 peptides, 17 chains. Longest chain 25 peptides. Score 0.624 Round 3: 147 peptides, 16 chains. Longest chain 19 peptides. Score 0.623 Round 4: 153 peptides, 16 chains. Longest chain 18 peptides. Score 0.646 Round 5: 151 peptides, 16 chains. Longest chain 24 peptides. Score 0.638 Taking the results from Round 4 Chains 16, Residues 137, Estimated correctness of the model 89.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 6343 restraints for refining 3012 atoms. 5811 conditional restraints added. Observations/parameters ratio is 1.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2002 (Rfree = 0.000) for 3012 atoms. Found 103 (103 requested) and removed 7 (51 requested) atoms. Cycle 27: After refmac, R = 0.1860 (Rfree = 0.000) for 3108 atoms. Found 67 (106 requested) and removed 12 (53 requested) atoms. Cycle 28: After refmac, R = 0.1773 (Rfree = 0.000) for 3162 atoms. Found 61 (108 requested) and removed 17 (54 requested) atoms. Cycle 29: After refmac, R = 0.1707 (Rfree = 0.000) for 3206 atoms. Found 57 (109 requested) and removed 29 (54 requested) atoms. Cycle 30: After refmac, R = 0.1668 (Rfree = 0.000) for 3234 atoms. Found 74 (110 requested) and removed 17 (55 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.79 2.02 NCS extension: 8 residues added (3 deleted due to clashes), 3306 seeds are put forward Round 1: 153 peptides, 21 chains. Longest chain 15 peptides. Score 0.553 Round 2: 153 peptides, 17 chains. Longest chain 19 peptides. Score 0.628 Round 3: 151 peptides, 18 chains. Longest chain 19 peptides. Score 0.602 Round 4: 154 peptides, 19 chains. Longest chain 19 peptides. Score 0.595 Round 5: 160 peptides, 19 chains. Longest chain 19 peptides. Score 0.619 Taking the results from Round 2 Chains 18, Residues 136, Estimated correctness of the model 88.4 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 6458 restraints for refining 3109 atoms. 5877 conditional restraints added. Observations/parameters ratio is 1.54 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1877 (Rfree = 0.000) for 3109 atoms. Found 106 (106 requested) and removed 17 (53 requested) atoms. Cycle 32: After refmac, R = 0.1776 (Rfree = 0.000) for 3198 atoms. Found 77 (109 requested) and removed 15 (54 requested) atoms. Cycle 33: After refmac, R = 0.1712 (Rfree = 0.000) for 3259 atoms. Found 77 (111 requested) and removed 26 (55 requested) atoms. Cycle 34: After refmac, R = 0.1676 (Rfree = 0.000) for 3309 atoms. Found 64 (113 requested) and removed 43 (56 requested) atoms. Cycle 35: After refmac, R = 0.1626 (Rfree = 0.000) for 3330 atoms. Found 65 (114 requested) and removed 33 (57 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.79 2.02 NCS extension: 20 residues added (1 deleted due to clashes), 3386 seeds are put forward Round 1: 138 peptides, 19 chains. Longest chain 16 peptides. Score 0.525 Round 2: 152 peptides, 18 chains. Longest chain 17 peptides. Score 0.606 Round 3: 147 peptides, 18 chains. Longest chain 20 peptides. Score 0.585 Round 4: 149 peptides, 16 chains. Longest chain 21 peptides. Score 0.630 Round 5: 152 peptides, 15 chains. Longest chain 21 peptides. Score 0.659 Taking the results from Round 5 Chains 17, Residues 137, Estimated correctness of the model 90.1 % 2 chains (24 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 6500 restraints for refining 3144 atoms. 5897 conditional restraints added. Observations/parameters ratio is 1.53 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1947 (Rfree = 0.000) for 3144 atoms. Found 107 (107 requested) and removed 33 (53 requested) atoms. Cycle 37: After refmac, R = 0.1748 (Rfree = 0.000) for 3217 atoms. Found 88 (110 requested) and removed 11 (55 requested) atoms. Cycle 38: After refmac, R = 0.1651 (Rfree = 0.000) for 3294 atoms. Found 80 (112 requested) and removed 34 (56 requested) atoms. Cycle 39: After refmac, R = 0.1590 (Rfree = 0.000) for 3336 atoms. Found 73 (114 requested) and removed 41 (57 requested) atoms. Cycle 40: After refmac, R = 0.1572 (Rfree = 0.000) for 3365 atoms. Found 78 (115 requested) and removed 40 (57 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.79 2.02 NCS extension: 12 residues added (3 deleted due to clashes), 3421 seeds are put forward Round 1: 128 peptides, 19 chains. Longest chain 14 peptides. Score 0.477 Round 2: 143 peptides, 17 chains. Longest chain 22 peptides. Score 0.587 Round 3: 144 peptides, 18 chains. Longest chain 21 peptides. Score 0.572 Round 4: 142 peptides, 20 chains. Longest chain 17 peptides. Score 0.523 Round 5: 147 peptides, 15 chains. Longest chain 20 peptides. Score 0.641 Taking the results from Round 5 Chains 15, Residues 132, Estimated correctness of the model 89.1 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 19184 reflections ( 99.72 % complete ) and 6771 restraints for refining 3176 atoms. 6238 conditional restraints added. Observations/parameters ratio is 1.51 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1855 (Rfree = 0.000) for 3176 atoms. Found 108 (108 requested) and removed 12 (54 requested) atoms. Cycle 42: After refmac, R = 0.1701 (Rfree = 0.000) for 3271 atoms. Found 98 (112 requested) and removed 6 (56 requested) atoms. Cycle 43: After refmac, R = 0.1587 (Rfree = 0.000) for 3363 atoms. Found 60 (115 requested) and removed 27 (57 requested) atoms. Cycle 44: After refmac, R = 0.1529 (Rfree = 0.000) for 3396 atoms. Found 65 (116 requested) and removed 23 (58 requested) atoms. Cycle 45: After refmac, R = 0.1501 (Rfree = 0.000) for 3437 atoms. Found 49 (117 requested) and removed 39 (58 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.80 2.03 NCS extension: 17 residues added (2 deleted due to clashes), 3468 seeds are put forward Round 1: 129 peptides, 19 chains. Longest chain 14 peptides. Score 0.482 Round 2: 139 peptides, 15 chains. Longest chain 19 peptides. Score 0.609 Round 3: 135 peptides, 17 chains. Longest chain 17 peptides. Score 0.553 Round 4: 135 peptides, 17 chains. Longest chain 17 peptides. Score 0.553 Round 5: 135 peptides, 18 chains. Longest chain 17 peptides. Score 0.532 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 18, Residues 124, Estimated correctness of the model 87.3 % 4 chains (34 residues) have been docked in sequence Sequence coverage is 27 % Consider running further cycles of model building using 2prx-2_warpNtrace.pdb as input Building loops using Loopy2018 18 chains (124 residues) following loop building 4 chains (34 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 19184 reflections ( 99.72 % complete ) and 7050 restraints for refining 3307 atoms. 6452 conditional restraints added. Observations/parameters ratio is 1.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1766 (Rfree = 0.000) for 3307 atoms. Found 0 (113 requested) and removed 3 (56 requested) atoms. Cycle 47: After refmac, R = 0.1687 (Rfree = 0.000) for 3303 atoms. Found 0 (113 requested) and removed 0 (56 requested) atoms. Cycle 48: After refmac, R = 0.1649 (Rfree = 0.000) for 3303 atoms. Found 0 (113 requested) and removed 0 (56 requested) atoms. Cycle 49: After refmac, R = 0.1630 (Rfree = 0.000) for 3302 atoms. Found 0 (113 requested) and removed 1 (56 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:11:24 GMT 2018 Job finished. TimeTaking 48.59 Used memory is bytes: 8979536